https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Ralf+Stephan 2026-09-13T03:54:41Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User:Ralf_Stephan&diff=1295344 2011-09-10T15:50:00Z

<p>Ralf Stephan: </p> <hr /> <div>Former IT specialist, now private biocurator from Berlin, interested in visualisation and molecular biology.<br /> <br /> *[[User:Ralf Stephan/Sandbox 1]]<br /> *[[User:Ralf Stephan/Sandbox 2]]<br /> <br /> Interesting categories:<br /> *[http://proteopedia.org/wiki/index.php?title=Special:Categories&amp;offset=Abc&amp;limit=50 starting with Abc]<br /> *[http://proteopedia.org/wiki/index.php?title=Special:Categories&amp;offset=Atp&amp;limit=100 starting with Atp]<br /> *[http://proteopedia.org/wiki/index.php?title=Special:Categories&amp;offset=Ion&amp;limit=50 starting with Ion]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=1295343 2011-09-10T15:38:07Z

<p>Ralf Stephan: /* Stage 2: Rehydration */ alt view</p> <hr /> <div>[[Image:1amj.png|left|200px|thumb|Crystal Structure of Bovine Aconitase, [[1amj]]]]<br /> {{STRUCTURE_1amj| PDB=1amj | SIZE=300| SCENE=Aconitase/Cv/1 |right|CAPTION=Bovine Aconitase, [[1amj]] }}<br /> <br /> [[Aconitase]] '''(ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> The images at the left and at the right correspond to one representative Aconitase, ''i.e.'' the crystal structure of Bovine Aconitase ([[1amj]]).<br /> In most organisms, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> Aconitase contains a Fe4S4 cluster which converts to Fe3S4 when the enzyme is inactive. In humans, two types of ACO are expressed: the soluble ACO1 and the mitochondrial ACO2.<br /> Aconitase from pig (PDB [[7acn]]) is a single polypeptide (M&lt;sub&gt;r&lt;/sub&gt; 83kD) that catalyzes the reversible isomerization of citrate and isocitrate.&lt;ref name=&quot;Zheng&quot;&gt;PMID 1313811&lt;/ref&gt; It is the second enzyme in the Citric acid cycle, which is a series of enzyme-catalysed chemical reactions that is crucial to aerobic cellular respiration and the production of ATP. <br /> <br /> ==Structure==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='right' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;<br /> The &lt;scene name='Anthony_Noles_Sandbox/Secondary_structure/1'&gt;secondary structure&lt;/scene&gt; consists of numerous alternating alpha helices and beta sheets (SCOP classification α/β alternating). The tertiary structure is somewhat bilobed with the active site in the middle, and, since there is only one subunit, there is no quaternary structure. Aconitase consists of four domains, three of which are tightly packed while the fourth is more flexible. &lt;ref name=&quot;Frishman&quot;&gt;PMID 8706708&lt;/ref&gt; Aconitase contains a &lt;scene name='Anthony_Noles_Sandbox/Fe-scluster/2'&gt;4Fe-4S iron-sulfur cluster&lt;/scene&gt;. This iron sulfur cluster does not participate in redox as most do, but holds the OH group of citrate to facilitate its elimination.&lt;ref&gt;PMID:16407072 &lt;/ref&gt; It is at this 4Fe-4S site that catalysis occurs and citrate or &lt;scene name='Anthony_Noles_Sandbox/Fe-scluster_bound_isocitrate/8'&gt;isocitrate&lt;/scene&gt; is bound. The rest of the &lt;scene name='Anthony_Noles_Sandbox/Fe-scluster_w_active_site/5'&gt;active site (manually rotate this scene to see the proximity of each residue to the 4Fe-4S cluster)&lt;/scene&gt; is made up of residues Gln72, Asp100, His101, Asp165, Ser166, His167, His147, Glu262, Asn258, Cys358, Cys421, Cys424, Cys358, Cys421, Asn446, Arg447, Arg452, Asp568, Ser642, Ser643, Arg644, Arg580. &lt;ref name=&quot;Beinert&quot;&gt;Beinert, H., Kennedy, M. C., Stout, C.D. “Aconitase as Iron−Sulfur Protein, Enzyme, and Iron-Regulatory Protein.” Chem. Rev. 1996, 96, 2335−2373.&lt;/ref&gt;<br /> <br /> {{Clear}}<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4/2'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/3'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/4'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt; together with a water molecule.This Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> Substrate-free aconitase contains a [4Fe-4S]&lt;sup&gt;2+&lt;/sup&gt; cluster with hydroxyl bound to one of the Fe. Upon binding of substrate the bound hydroxyl is protonated. A hydrogen bond from &lt;scene name='Anthony_Noles_Sandbox/His101/3'&gt;His101&lt;/scene&gt; to the isocitrate hydroxyl is donated to form water. Alternatively, the proton could be donated by &lt;scene name='Anthony_Noles_Sandbox/His167/3'&gt;His167&lt;/scene&gt; as this histidine is hydrogen bonded to a H&lt;sub&gt;2&lt;/sub&gt;O molecule. His167 is also hydrogen bonded to the bound H&lt;sub&gt;2&lt;/sub&gt;O in the [4Fe-4S] cluster. Both &lt;scene name='Anthony_Noles_Sandbox/His_101_and_167/4'&gt;His101 and His167&lt;/scene&gt; are paired with carboxylates (&lt;scene name='Anthony_Noles_Sandbox/Asp100_and_glu262/3'&gt;Asp100 and Glu262&lt;/scene&gt;, respectively) and are likely to be protonated. The conformational change associated with substrate binding reorients the cluster. &lt;ref name=&quot;Beinert&quot; /&gt; The residue which removes a proton from citrate or isocitrate is &lt;scene name='Anthony_Noles_Sandbox/Ser642/4'&gt;Ser642&lt;/scene&gt;. &lt;ref name=&quot;Beinert&quot; /&gt; This causes the cis-Aconitate intermediate (seen below), which consists of a double bond, which is a direct result of the deprotonation. Then, there is a rehydration of the double bond of cis-aconitate to form isocitrate (if the original substrate was citrate). To better understand this, consider this process as stages, seen below. <br /> {{Clear}}<br /> ====Stage 1: Dehydration====<br /> First, dehydration of citrate causes a proton and OH group to be removed from only the 'lower arm'.&lt;ref name=&quot;Voet&quot;&gt;Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley &amp; Sons, 2008. p. 578-579. Print.&lt;/ref&gt; This forms a cis-Aconitate intermediate. <br /> <br /> ====Stage 2: Rehydration====<br /> The second main stage of the reaction is the rehydration of the cis-Aconitate intermediate. This forms isocitrate. It is catalyzed in a stereospecific way such that only one isocitrate stereoisomer is formed. &lt;ref name=&quot;Voet&quot; /&gt;<br /> <br /> Thus, the overall reaction that aconitase catalyzes is: Citrate ←→cis-Aconitate←→Isocitrate, as seen below:<br /> [[ Image:Aconitase.JPG]]<br /> <br /> A more stereochemical view at the reaction shows that the aconitate intermediate has to make a 180 degree flip in order to start the other half of the reaction:<br /> [[Image:Aconitase steps stereo.png|400px]]<br /> <br /> ==Regulation==<br /> Aconitase can be inhibited or activated to increase or decrease the ability to catalyze the reaction of citrate to isocitrate. The activity of aconitase can be reduced when one Fe is lost from the cluster. This lowers the activity over 100-fold, but then can regain full activity by adding another Fe from solution. &lt;ref name=&quot;Flint&quot;&gt;Flint, DH., and Allen, RM. &quot;Iron-sulfur protein with nonredox functions.” Chem. Rev. 1996, 96, 2315−2334.&lt;/ref&gt; Aconitase is also strongly inhibited by nitro analogs &lt;ref name=&quot;Flint&quot; /&gt;<br /> <br /> The Citric Acid Cycle works in such a way that the product of one reaction becomes the reactant of another, with different enzymes catalyzing each reaction. Aconitase is one such enzyme. Some of these enzymes are tightly regulated, either activated or inhibited, by the concentration of reactant, product, ATP or NADH, and thus are rate-determining. Aconitase is not one of the three rate-determining enzymes of the Citric Acid Cycle as its ΔG is not negative (ΔG°′≈5 kJ/mol and ΔG≈0 kJ/mol).&lt;ref name=&quot;Voet&quot; /&gt; Aconitase functions close to equilibrium and the rate of citrate consumption depends on the activity of NAD&lt;sup&gt;+&lt;/sup&gt;-dependent isocitrate dehydrogenase, which is one of the three rate-determining enyzmes. Isocitrate dehydrogenase uses the product of the reaction aconitase catalyzes. Both Citrate synthase and Isocitrate dehydogenase are inhibited by NADH concentration, but aconitase itself is not.&lt;ref name=&quot;Voet&quot; /&gt; Since the rate of aconitase depends on the activity of NAD&lt;sup&gt;+&lt;/sup&gt;-dependent isocitrate dehydrogenase, then citrate could build up on the reactant side, which would then inhibit the enzyme of the previous step, citrate synthase. An illustration of this is seen below, with the boxes representing the enzymes that are catalyzing each reaction. This is a common example of how the Citric Acid Cycle works in order to produce ATP without wasting resources. Similar inhibition/activation of enzymes occurs based on concentrations of ATP, NADH, Calcium, CoA, and others. <br /> [[ Image:Regulation.JPG]]<br /> <br /> <br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> <br /> Along with serving as a catalyst, aconitase is a member of the iron regulatory protien-1 (IRP-1) family. These enzymes have been found to play a role in regulatory RNA-binding proteins. This suggests a novel role for Fe-S clusters as post-translational regulatory switches.&lt;ref name=&quot;Frishman&quot; /&gt;<br /> {{Clear}}<br /> == Available 3D structures of Aconitase==<br /> <br /> === ACO ===<br /> <br /> <br /> [[1b0k]] – pACO (mutant) – pig&lt;br /&gt;<br /> [[5acn]] – pACO+Fe3S4&lt;br /&gt;<br /> [[6acn]] - pACO+Fe4S4&lt;br /&gt;<br /> [[1amj]], [[1nit]] – cACO - cow&lt;br /&gt;<br /> <br /> <br /> === ACO+citrate ===<br /> <br /> <br /> [[1c96]] - pACO (mutant)+citrate&lt;br /&gt;<br /> [[1b0m]] - pACO (mutant)+fluorocitrate&lt;br /&gt;<br /> <br /> <br /> === ACO+aconitate ===<br /> <br /> <br /> [[1fgh]] – cACO+4-hydroxy-aconitate &lt;br /&gt;<br /> [[1aco]] – cACO+transaconitate&lt;br /&gt; <br /> [[1nis]] - cACO+transaconitate+nitrocitrate&lt;br /&gt;<br /> <br /> <br /> === ACO+isocitrate ===<br /> <br /> <br /> [[7acn]] - pACO +isocitrate&lt;br /&gt;<br /> [[1c97]], [[1b0j]] - pACO (mutant)+isocitrate&lt;br /&gt;<br /> [[1ami]], [[8acn]] – cACO+isocitrate&lt;br /&gt;<br /> <br /> <br /> === ACO1 ===<br /> <br /> <br /> [[2b3x]], [[2b3y]] – hACO1 – human&lt;br /&gt;<br /> [[2ipy]] – rACO1 (mutant)+ferritin H IRE-RNA – rabbit&lt;br /&gt;<br /> <br /> <br /> === ACO2 ===<br /> <br /> <br /> [[1l5j]] – ACO2 – ''Escherichia coli''&lt;br /&gt;<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> ==Additional Resources==<br /> For additional information, see: [[Carbohydrate Metabolism]]<br /> &lt;br /&gt;<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]<br /> <br /> [[Category:Topic Page]]</div>

Ralf Stephan https://proteopedia.org/index.php?title=File:Aconitase_steps_stereo.png&diff=1295342 2011-09-10T15:35:38Z

<p>Ralf Stephan: stereochemical view of aconitase reaction</p> <hr /> <div>stereochemical view of aconitase reaction</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=937514 2009-03-19T08:35:40Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4/2'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/3'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/4'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt; together with a water molecule.This Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=937513 2009-03-19T08:23:20Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4/2'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/3'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/4'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=937512 2009-03-19T08:22:24Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4/2'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/4'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=937511 2009-03-19T08:20:03Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4/3'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/4'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=934494 2009-03-08T06:57:08Z

<p>Ralf Stephan: literature</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-morph/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/2'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Literature ==<br /> * M. Claire Kennedy and Helmut Beinert: ''IX.4. Aconitase.'' in Ivano Bertini, Harry B. Gray, Edward I. Stiefel, Joan Selverstone Valentine (eds.): ''Biological Inorganic Chemistry: Structure and Reactivity.'' University Science Books, Herndon 2006. ISBN 1891389432 pp.209--<br /> <br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=User_talk:Ralf_Stephan&diff=934393 2009-03-07T08:09:13Z

<p>Ralf Stephan: /* odd changes in scenes */</p> <hr /> <div>'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! [[User:Eran Hodis|Eran Hodis]] 14:14, 6 February 2009 (IST)<br /> <br /> == Morphs ==<br /> <br /> Hi Ralf,<br /> <br /> Eventually you might want to consider adding morphs to give the idea of the conformational changes in the transport proteins between their open and closed states. An example can be found on the [[Proton Channels]] page that Eric Martz created. The morph itself does not represent the actual motion between the two states -- open and closed -- but rather is a linear interpolation (in most morphs) between the starting structure and the ending structure.<br /> <br /> Best,<br /> [[User:Eran Hodis|Eran Hodis]] 18:37, 6 February 2009 (IST)<br /> <br /> :Yes, actually, I chose my first protein after I had a good look at the Yale gallery what they had. I'm aware of the scarcity of structures. Thanks. --[[User:Ralf Stephan|Ralf Stephan]] 18:41, 6 February 2009 (IST)<br /> <br /> <br /> ==Reponse==<br /> <br /> Hi Ralf, I responded on my user talk page. Best, --[[User:Eran Hodis|Eran Hodis]] 02:35, 8 February 2009 (IST)<br /> <br /> == Wikipedia link to Metalloproteases ==<br /> <br /> In regards to a Wikipedia link to the page on metalloproteases, please see [[Proteopedia:Policy#Links_to_Wikipedia]]. You're welcome to help shape this policy, but our current thinking is that if the link is to a page that could benefit from 3D images, then we should link to the page in Proteopedia (even if it doesn't exist, to encourage creation), and that page can then link to Wikipedia. --[[User:Eran Hodis|Eran Hodis]] 12:34, 8 February 2009 (IST)<br /> :No, you're right, the german language entry is much better. I'll translate it for Proteopedia. --[[User:Ralf Stephan|Ralf Stephan]] 12:36, 8 February 2009 (IST)<br /> <br /> == Gzipped PDBS ==<br /> <br /> You should now be able to upload gzipped PDBs --[[User:Eran Hodis|Eran Hodis]] 19:08, 17 February 2009 (IST)<br /> :Great, many thanks! --[[User:Ralf Stephan|Ralf Stephan]] 20:55, 17 February 2009 (IST)<br /> <br /> == Internal links in Applet captions ==<br /> <br /> Hi Ralf,<br /> Fixed this problem. Thanks for pointing out bugs that are simple to fix!<br /> --[[User:Eran Hodis|Eran Hodis]] 19:20, 18 February 2009 (IST)<br /> :Thanks for fixing, anyway! --[[User:Ralf Stephan|Ralf Stephan]] 20:03, 18 February 2009 (IST)<br /> <br /> == odd changes in scenes ==<br /> <br /> Regarding this problem you brought up:<br /> :problems with scenes changing unexpectedly appear in the first applet on the aconitase (older version) page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --Ralf Stephan 18:37, 21 February 2009 (IST)<br /> <br /> I confirm that I see the problem too. Are you using the SAT to create your scenes or do you right click on the Jmol, open up the console and type commands into Jmol by hand? --[[User:Eran Hodis|Eran Hodis]] 00:42, 7 March 2009 (IST)<br /> :Scene 3 was built using the console. Is it not recommended? Not everything is possible with SAT. --[[User:Ralf Stephan|Ralf Stephan]] 10:09, 7 March 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=File:5acn-7acn-sf4morph.pdb.gz&diff=934367 2009-03-06T17:57:36Z

<p>Ralf Stephan: /* Summary */</p> <hr /> <div>== Summary ==<br /> Linear morph between 5acn and 7acn, hiding everything except SF3/SF4 and residues 358,421,424 and HOH.<br /> <br /> == Licensing ==<br /> {{PD-self}}</div>

Ralf Stephan https://proteopedia.org/index.php?title=Openbabel&diff=934366 2009-03-06T17:53:34Z

<p>Ralf Stephan: New page: &#039;&#039;&#039;Openbabel&#039;&#039;&#039; is a framework for reading, manipulating, and writing molecules that understands many possible file formats and is able to convert between them. The framework is written in...</p> <hr /> <div>'''Openbabel''' is a framework for reading, manipulating, and writing molecules that understands many possible file formats and is able to convert between them. The framework is written in C++ but can be used also in the Python language (the name of the wrapper is '''pybel''').<br /> <br /> Usage of openbabel is free. Publication of code linked to openbabel is restricted to the GNU public license GPL.<br /> <br /> == External links ==<br /> *http://openbabel.org</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=934365 2009-03-06T17:30:41Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-morph/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/2'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=934364 2009-03-06T17:29:42Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-morph/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-morph/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. On activation of the enzyme, &lt;scene name='Aconitase/7acn-morph/1'&gt;a fourth iron atom is included in the cluster&lt;/scene&gt;. It can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=File:5acn-7acn-sf4morph.pdb.gz&diff=934362 2009-03-06T17:14:12Z

<p>Ralf Stephan: Morph between 5acn and 7acn, hiding everything except SF3/SF4 and residues 358,421,424 and HOH.</p> <hr /> <div>== Summary ==<br /> Morph between 5acn and 7acn, hiding everything except SF3/SF4 and residues 358,421,424 and HOH.<br /> == Licensing ==<br /> {{PD-self}}</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=934315 2009-03-05T08:51:08Z

<p>Ralf Stephan: under construction</p> <hr /> <div>UNDER CONSTRUCTION<br /> <br /> '''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/6'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=934103 2009-03-04T16:45:40Z

<p>Ralf Stephan: /* Pages About Molecules (Not Titled with a PDB Code) */ order</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[Rop protein]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[SelB Recognition]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Serum Paraoxonase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Transcription Termination Factor Rho]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[VirE1/VirE2]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932654 2009-03-04T11:19:11Z

<p>Ralf Stephan: fix</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> ===A - C===<br /> *[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[Rop protein]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[SelB Recognition]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Serum Paraoxonase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Transcription Termination Factor Rho]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[VirE1/VirE2]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932653 2009-03-04T11:16:47Z

<p>Ralf Stephan: /* Pages About Molecules (Not Titled with a PDB Code) */ fix</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> *[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[Rop protein]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[SelB Recognition]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Serum Paraoxonase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Transcription Termination Factor Rho]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[VirE1/VirE2]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932652 2009-03-04T11:14:22Z

<p>Ralf Stephan: /* Pages About Molecules (Not Titled with a PDB Code) */ a bit reordering</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> *[[A Physical Model of the β2-Adrenergic Receptor|β2-Adrenergic Receptor, A Physical Model of the]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[Rop protein]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[SelB Recognition]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Serum Paraoxonase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Transcription Termination Factor Rho]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[VirE1/VirE2]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932388 2009-03-03T19:12:47Z

<p>Ralf Stephan: /* R - Z */ and some</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[Rop protein]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[SelB Recognition]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Serum Paraoxonase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Transcription Termination Factor Rho]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[VirE1/VirE2]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932387 2009-03-03T19:04:55Z

<p>Ralf Stephan: /* D - L */ +1</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Ion channels]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932386 2009-03-03T19:04:20Z

<p>Ralf Stephan: /* M - P */ add some</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Metalloproteases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[NADH quinone oxidoreductase (NQO1) with inhibitor dicoumarol|NADH quinone oxidoreductase (NQO1)]]<br /> *[[Nucleosomes]]<br /> *[[OhrR]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[PcrA helicase]]<br /> *[[Personal favorites]]<br /> *[[Phosphoglucose isomerase]]<br /> *[[Photosystem II]]<br /> *[[Prion protein]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> *[[Pyruvate phosphate dikinase]]<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932384 2009-03-03T18:26:14Z

<p>Ralf Stephan: /* R - Z */ +2</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[Nucleosomes]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[Personal favorites]]<br /> *[[Photosystem II]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[Human RecQ-Like protein 1|RecQ-Like protein 1, human]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Herpes Simplex Virus Thymidine Kinase|Thymidine Kinase, Herpes Simplex Virus]]<br /> *[[Zinc Fingers]]<br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932383 2009-03-03T18:23:57Z

<p>Ralf Stephan: /* D - L */ add a few</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[DNA-binding protein VirE2 from Agrobacterium tumefaciens complexed with chaperone VirE1|DNA-binding protein VirE2 (''Agrobacterium'')]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Doppel]]<br /> *[[Dronpa]]<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Lac repressor]]<br /> *[[Lactose Permease]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[Nucleosomes]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[Personal favorites]]<br /> *[[Photosystem II]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Zinc Fingers]]<br /> <br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932382 2009-03-03T18:10:16Z

<p>Ralf Stephan: /* A - C */ added a few</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> **[[AChE bivalent inhibitors|AChE bivalent inhibitors, Part I]], [[AChE bivalent inhibitors (Part II)|Part II]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Alpha-1-antitrypsin]]<br /> *[[Antizyme Inhibitor]]<br /> *[[A Physical Model of the β2-Adrenergic Receptor]]<br /> *[[ATP Phosphoribosyl Transferase]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Biotin Protein Ligase]]<br /> *[[Chitinases]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Lac repressor]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[Nucleosomes]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[Personal favorites]]<br /> *[[Photosystem II]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Zinc Fingers]]<br /> <br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Topic_Pages&diff=932371 2009-03-03T10:14:42Z

<p>Ralf Stephan: added start/end topics markers</p> <hr /> <div>[[Topic pages]] are pages about proteins or molecules or families of proteins or molecules that are not named with a [[PDB]] code. [[Proteopedia]] contains a page for each entry in the PDB, created automatically, and these pages generally describe a particular solved structure. A topic page like [[hemoglobin]], however, will address the protein in general, and refer to several solved structures such as [[1gzx]] and [[2hbs]]. And so, topic pages can be thought of as higher up in the heirarchy of page organization in Proteopedia than are PDB-code-titled pages. They are also never created automatically.<br /> <br /> ==Pages About Molecules (Not Titled with a PDB Code)==<br /> <br /> The list below is intended to include all pages about molecules or families of molecules that are not named with a PDB code, and that also have substantial content. Because this list is manually maintained, it may be out of date. For comparison, here is an automatically generated list of [[Special:Allpages/a | all pages whose titles do not begin with a numeral]], and here is a list of [[Special:Allpages | all pages]].<br /> <br /> &lt;big&gt;'''See also: [[About Macromolecular Structure]]'''&lt;/big&gt;, a list of pages not listed below.<br /> <br /> &lt;!-- Start of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ===A - C===<br /> *[[AChE inhibitors and substrates]]<br /> *[[Acetylcholine]]<br /> *[[Acetylcholinesterase]]<br /> *[[Acid-beta-glucosidase]]<br /> &lt;!-- *[[Antibodies]] --&gt;<br /> *[[Antizyme Inhibitor]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *[[Bacterial Intein-Like Domains (BILs)]]<br /> *[[Believe It or Not!]]<br /> *[[Cyt2Ba]]<br /> <br /> ===D - L===<br /> *[[DHFR]]<br /> *[[Dihydrofolate reductase]]<br /> *[[DNA]]<br /> *[[Structure of E. coli DnaC helicase loader|DnaC helicase loader, structure of (''E. coli'')]] (homology model)<br /> *[[Eran Hodis's Favorites]]<br /> *[[Eric Martz's Favorites]]<br /> &lt;!-- *[[Fibrin]] --&gt;<br /> *[[Glycine]]<br /> *[[Green Fluorescent Protein]]<br /> *[[Heme]]<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]]<br /> *[[Hint auto-proteolytic protein-processing domains]]<br /> *[[Lac repressor]]<br /> <br /> ===M - P===<br /> *[[Major Histocompatibility Complex Class I]]: Crucial to your defenses against viruses, and one of the [[Highest impact structures | Highest Impact Structures of All Time]]<br /> *[[Matrix metalloproteinases]]<br /> *[[Morphs]] of conformational changes of macromolecules<br /> *[[Nucleosomes]]<br /> *[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|p19 Suppression of RNA Silencing]]<br /> *[[P53]]<br /> *[[Personal favorites]]<br /> *[[Photosystem II]]<br /> *[[Proton Channels]] (Includes an animated morph)<br /> <br /> ===R - Z===<br /> *[[Recoverin, a calcium-activated myristoyl switch]]<br /> *[[SGAP]]<br /> *[[Scene authoring tools]]<br /> *[[Serine Protease]]<br /> *[[Serine hydrolase]]<br /> *[[Site | Sites, Functional]]<br /> *[[Strictisidine Synthase]]<br /> *[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]<br /> *[[TATA-Binding Protein]]<br /> *[[Teaching Strategies Using Proteopedia]]<br /> *[[Zinc Fingers]]<br /> <br /> &lt;!-- End of topic pages. Please DON'T REMOVE --&gt;<br /> <br /> ----<br /> <br /> ==PDB Code Pages==<br /> Here is a manually maintained list of pages titled with PDB codes that have especially well-developed content.<br /> <br /> *[[1d9z]] The DNA repair protein UVRB in complex with ATP<br /> *[[1eve]] Acetylcholinesterase complexed with the anti-Alzheimer's disease drug Aricept.<br /> *[[1mr4]] Antifungal and insecticidal protein NaD1 from ''Nicotiana''<br /> *[[1n4n]] Defensin from ''Petunia''<br /> *[[1ogs]] Human acid-beta-glucosidase<br /> *[[1v04]] Paraoxonase-1 via directed evolution<br /> *[[1xjo]] Aminopeptidase<br /> <br /> <br /> *[[2cek]] ''Torpedo californica'' acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug.<br /> *[[2ic8]] ''Escherichia coli'' GlpG, an integral membrane protein that belongs to the widespread rhomboid protease family<br /> *[[2p18]] ''Leishmania infantum'' Glyoxalase II<br /> *[[2rd0]] Phosphatidylinositol kinase oncogene, with many figures from the publication rendered in Jmol.<br /> *[[2rkx]] Chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase<br /> *[[2v9d]] A prophage protein belonging to the dihydrodipicolinic acid synthase family<br /> *[[2veo]] X-ray structure of ''Candida antarctica'' lipase A in its closed state<br /> <br /> <br /> *[[5p21]] The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930927 2009-02-22T18:23:57Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/6'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930924 2009-02-22T18:10:02Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */ lf</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[User:Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)<br /> <br /> '''problems with scenes changing unexpectedly''' appear in the first applet on the [http://proteopedia.org/wiki/index.php?title=Aconitase&amp;oldid=930869 aconitase (older version)] page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930923 2009-02-22T18:09:24Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */ lf</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[User:Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)<br /> <br /> '''problems with scenes changing unexpectedly''' appear in the first applet on the [http://proteopedia.org/wiki/index.php?title=Aconitase&amp;oldid=930869|aconitase (older version)] page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=User:Ralf_Stephan/Sandbox_1&diff=930922 2009-02-22T17:43:41Z

<p>Ralf Stephan: test script</p> <hr /> <div>&lt;applet load=7acd scene='User:Ralf_Stephan/Sandbox_1/Test/1' /&gt;</div>

Ralf Stephan https://proteopedia.org/index.php?title=Major_Facilitators&diff=930898 2009-02-22T10:46:14Z

<p>Ralf Stephan: /* Available structures */ +1</p> <hr /> <div>'''Major Facilitators''' are membrane proteins that help with both influx and outflux of specific small molecules. They are neither passive channels, nor do they active pumping, like the ATPases. Like a rocker-switch, they tilt between the two states 'outside open' and 'inside open'. This tilting (or switching) is triggered when a molecule has docked inside, and it transports the molecule to the other side. There are major facilitator uniporters, symporters, and antiporters. Antiporters usually transport a second, different, molecule, when switching back in the opposite direction. In 2009, there is still no structure data that would clearly show the transport process in major facilitators.<br /> <br /> == Classification ==<br /> TCDB, the most sophisticated classification of transport proteins to date, classifies the major facilitators as family 2.A.1 in the clan of '''secondary active [[porters]]'''.<br /> <br /> == Available structures ==<br /> The family has about 10,000 sequenced members from all living organisms. There are, however, only a few protein structures resolved.<br /> * from ''E.&amp;nbsp;coli'' K12:<br /> ** the [[glycerol-3-phosphate transporter]] ([[1pw4]])<br /> ** the [[multidrug resistance protein]] EmrD ([[2gfp]])<br /> ** the [[Lactose Permease|lactose permease]] ([[1pv7]], [[2cfp]], [[2cfq]], [[2v8n]])<br /> * from ''Clostridum phytofermentans'': the sugar transporter ([[3brs]])<br /> <br /> == Weblinks ==<br /> *[http://www.tcdb.org/ The TCDB database]<br /> *[http://www.tcdb.org/tcdb/subclass2.php?tc=2.A.1 TCDB: 2.A.1 The Major Facilitator Superfamily (MFS)]<br /> *[http://www.tcdb.org/pdb_structure.php TCDB: Transport proteins with PDB structures]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Ion_channels&diff=930897 2009-02-22T10:32:13Z

<p>Ralf Stephan: /* Available structures */ +2</p> <hr /> <div>'''Ion channels''' are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the [[natrium channels]], or the [[chloride channels]]. Some, like the [[TRP channels]], let through a bunch of cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). Finally, ion channels are the fastest of all membrane transporters, with 10^6 to 10^8 transported units per second versus 10^2 to 10^4 molecules per second for porters/carriers, or 10^0 to 10^3 for ATP-driven pumps.<br /> <br /> == Classification ==<br /> TCDB, the most sophisticated classification of transport proteins to date, classify ion channels as a heterogenous subset of all '''&amp;alpha;-type channels''', whose singular property is to consist mainly of [[alpha helix|&amp;alpha;-helices]] that span the membrane. They are distinct in this from the [[beta-barrel porins]], the [[pore-forming toxins]], but also from non-ribosomally synthesized channels like [[gramicidin]], [[polyglutamine]] or [[digitoxin]]. All these proteins are '''passive''' transport proteins.<br /> <br /> == Available structures ==<br /> Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no surprise that there are preciously few structure data for ion channels. At the moment, the following &amp;alpha;-type ion channels have been at least partly resolved:<br /> * the [[voltage-dependent potassium channel]] K&lt;sub&gt;v&lt;/sub&gt;1 from ''Rattus norvegicus'' ([[1qrq]], [[1exb]], [[1t1d]], [[2a79]], [[2r9r]], [[3eau]], [[3eb3]], [[3eb4]])<br /> * the [[voltage-dependent calcium channel]] from ''Rattus norvegicus'' (L-type: [[1t0h]], [[1t0j]], [[1vyt]], [[1vyu]], [[1vyv]], [[2vay]], [[3bxk]], R-type: [[3bxl]])<br /> * the [[voltage-gated potassium channel]] KcsA from ''Streptomyces lividans'' and ''Mus musculus'' with the structures [[1bl8]], [[1k4c]], [[1k4d]], [[2bob]], [[2boc]], [[2hg5]],[[2h8p]], [[2hfe]], [[2itc]], [[2itd]], [[2k1e]], [[2nlj]]<br /> * the [[voltage-gated potassium channel]] K&lt;sub&gt;v&lt;/sub&gt;AP from ''Aeropyrum pernix'' ([[1orq]], [[2a0l]]), and human K&lt;sub&gt;v&lt;/sub&gt;7 ([[2ovc]], [[3bj4]])<br /> * the [[voltage-gated sodium channel]] Na&lt;sub&gt;v&lt;/sub&gt;1.2 ([[1byy]], [[2kav]]) and Na&lt;sub&gt;v&lt;/sub&gt;1.5 ([[2kbi]])<br /> * the [[calcium-gated potassium channel mthK]] from ''Methanobacterium thermoautotrophicum'' ([[1lnq]], [[2fy8]])<br /> * the hyperpolarization-activated and cyclic nucleotide-gated K+ channel [[HCN]] from ''Mus musculus'' ([[1q3e]], [[1q43]], [[1q5o]], [[2ptm]], [[2q0a]], [[3bpz]])<br /> * the [[inward rectifier potassium channels]] KirBac3.1 ([[1xl4]],[[1xl6]]) and Kir3.1 (Cyt. only: [[1n9p]], [[1u4e]], [[1u4f]], [[1p7b]], [[2e4f]])<br /> * the acid-sensitive (proton-gated) cation channel [[ASIC]] from ''Gallus gallus'' ([[2qts]])<br /> * the human [[intracellular chloride channel]] CLIC-2 ([[2per]], [[2r4v]], [[2r5g]])<br /> * the [[nicotinic acetylcholine-activated cation-selective channel]] from ''Torpedo marmorata'' ([[1oed]], [[2bg9]], [[2k58]], [[2k59]])<br /> * a [[potassium channel]] from ''Burkholderia pseudomallei'' ([[1p7b]])<br /> * the [[ammonium transporter]] from ''Archaeoglobus fulgidus'' ([[2b2f]]) and from ''Nitrosomonas europaea'' ([[3b9y]], [[3b9z]], [[3bhs]])<br /> * the small-conductance [[mechanosensitive channel]] from ''E.&amp;nbsp;coli'' K12 ([[2oau]], [[2vv5]], see also [[2k2b]])<br /> * [[TRP channels]] ([[2rfa]], [[3e7k]])<br /> * human [[phospholamban]] ([[1zll]], [[2hyn]])<br /> * the P7 [[viroporin]] of Hepatitis C virus ([[2k8j]])<br /> * the [[M2 protein]] from Influenza A ([[1nyj]], [[2kad]], [[2rlf]], [[3c9j]]) <br /> * [[aquaporins]] from several species:<br /> ** ''Methanobacterium thermoautotrophicum'' (aqpM, [[2evu]], [[2f2c]])<br /> ** ''E.&amp;nbsp;coli'' K12 (Aquaporin Z, [[1r2c]], [[2abm]])<br /> ** the [[glycerol uptake facilitator]] from ''E.&amp;nbsp;coli'' K12 (GlpF, [[1lda]], [[1ldf]], [[1ldi]], [[1fx8]])<br /> ** ''Homo sapiens'' (AQP-1, [[1fqy]], [[1ih5]])<br /> ** ''Bos taurus'' (Aquaporin-0, [[1ymg]], [[2b6p]])<br /> <br /> Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved:<br /> * [[Gramicidin]] ([[1av2]], [[1c4d]], [[1mag]])<br /> * fungal [[Antiamoebin]] ([[1joh]], [[1gq0]])<br /> * fungal [[Trichotoxin]] ([[1m24]])<br /> * further [[Peptaibol]] antibiotics ([[1ob4]], [[1ob6]], [[1ob7]])<br /> <br /> We do not count ClC chloride carriers as ion channels, as they are secondary active [[carriers]].<br /> <br /> == Weblinks ==<br /> *[http://www.tcdb.org/ The TCDB database]<br /> *[http://www.tcdb.org/tcdb/subclass2.php?tc=1.A TCDB: 1.A α-Type channels]<br /> *[http://www.tcdb.org/pdb_structure.php TCDB: Transport proteins with PDB structures]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Ion_channels&diff=930896 2009-02-22T10:29:37Z

<p>Ralf Stephan: /* Available structures */ +aquaporins</p> <hr /> <div>'''Ion channels''' are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the [[natrium channels]], or the [[chloride channels]]. Some, like the [[TRP channels]], let through a bunch of cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). Finally, ion channels are the fastest of all membrane transporters, with 10^6 to 10^8 transported units per second versus 10^2 to 10^4 molecules per second for porters/carriers, or 10^0 to 10^3 for ATP-driven pumps.<br /> <br /> == Classification ==<br /> TCDB, the most sophisticated classification of transport proteins to date, classify ion channels as a heterogenous subset of all '''&amp;alpha;-type channels''', whose singular property is to consist mainly of [[alpha helix|&amp;alpha;-helices]] that span the membrane. They are distinct in this from the [[beta-barrel porins]], the [[pore-forming toxins]], but also from non-ribosomally synthesized channels like [[gramicidin]], [[polyglutamine]] or [[digitoxin]]. All these proteins are '''passive''' transport proteins.<br /> <br /> == Available structures ==<br /> Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no surprise that there are preciously few structure data for ion channels. At the moment, the following &amp;alpha;-type ion channels have been at least partly resolved:<br /> * the [[voltage-dependent potassium channel]] K&lt;sub&gt;v&lt;/sub&gt;1 from ''Rattus norvegicus'' ([[1qrq]], [[1exb]], [[1t1d]], [[2a79]], [[2r9r]], [[3eau]], [[3eb3]], [[3eb4]])<br /> * the [[voltage-dependent calcium channel]] from ''Rattus norvegicus'' (L-type: [[1t0h]], [[1t0j]], [[1vyt]], [[1vyu]], [[1vyv]], [[2vay]], [[3bxk]], R-type: [[3bxl]])<br /> * the [[voltage-gated potassium channel]] KcsA from ''Streptomyces lividans'' and ''Mus musculus'' with the structures [[1bl8]], [[1k4c]], [[1k4d]], [[2bob]], [[2boc]], [[2hg5]],[[2h8p]], [[2hfe]], [[2itc]], [[2itd]], [[2k1e]], [[2nlj]]<br /> * the [[voltage-gated potassium channel]] K&lt;sub&gt;v&lt;/sub&gt;AP from ''Aeropyrum pernix'' ([[1orq]], [[2a0l]]), and human K&lt;sub&gt;v&lt;/sub&gt;7 ([[2ovc]], [[3bj4]])<br /> * the [[voltage-gated sodium channel]] Na&lt;sub&gt;v&lt;/sub&gt;1.2 ([[1byy]], [[2kav]]) and Na&lt;sub&gt;v&lt;/sub&gt;1.5 ([[2kbi]])<br /> * the [[calcium-gated potassium channel mthK]] from ''Methanobacterium thermoautotrophicum'' ([[1lnq]], [[2fy8]])<br /> * the hyperpolarization-activated and cyclic nucleotide-gated K+ channel [[HCN]] from ''Mus musculus'' ([[1q3e]], [[1q43]], [[1q5o]], [[2ptm]], [[2q0a]], [[3bpz]])<br /> * the [[inward rectifier potassium channels]] KirBac3.1 ([[1xl4]],[[1xl6]]) and Kir3.1 (Cyt. only: [[1n9p]], [[1u4e]], [[1u4f]], [[1p7b]], [[2e4f]])<br /> * the acid-sensitive (proton-gated) cation channel [[ASIC]] from ''Gallus gallus'' ([[2qts]])<br /> * the human [[intracellular chloride channel]] CLIC-2 ([[2per]], [[2r4v]], [[2r5g]])<br /> * the [[nicotinic acetylcholine-activated cation-selective channel]] from ''Torpedo marmorata'' ([[1oed]], [[2bg9]], [[2k58]], [[2k59]])<br /> * a [[potassium channel]] from ''Burkholderia pseudomallei'' ([[1p7b]])<br /> * the [[ammonium transporter]] from ''Archaeoglobus fulgidus'' ([[2b2f]]) and from ''Nitrosomonas europaea'' ([[3b9y]], [[3b9z]], [[3bhs]])<br /> * the small-conductance [[mechanosensitive channel]] from ''E.&amp;nbsp;coli'' K12 ([[2oau]], [[2vv5]], see also [[2k2b]])<br /> * [[TRP channels]] ([[2rfa]], [[3e7k]])<br /> * human [[phospholamban]] ([[1zll]], [[2hyn]])<br /> * the P7 [[viroporin]] of Hepatitis C virus ([[2k8j]])<br /> * the [[M2 protein]] from Influenza A ([[1nyj]], [[2kad]], [[2rlf]], [[3c9j]]) <br /> * [[aquaporins]] from several species:<br /> ** ''Methanobacterium thermoautotrophicum'' (aqpM, [[2evu]], [[2f2c]])<br /> ** ''E.&amp;nbsp;coli'' K12 (Aquaporin Z, [[1r2c]], [[2abm]])<br /> ** the [[glycerol uptake facilitator]] from ''E.&amp;nbsp;coli'' K12 ([[1ldi]], [[1fx8]])<br /> ** ''Homo sapiens'' (AQP-1, [[1fqy]], [[1ih5]])<br /> ** ''Bos taurus'' (Aquaporin-0, [[1ymg]], [[2b6p]])<br /> <br /> Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved:<br /> * [[Gramicidin]] ([[1av2]], [[1c4d]], [[1mag]])<br /> * fungal [[Antiamoebin]] ([[1joh]], [[1gq0]])<br /> * fungal [[Trichotoxin]] ([[1m24]])<br /> * further [[Peptaibol]] antibiotics ([[1ob4]], [[1ob6]], [[1ob7]])<br /> <br /> We do not count ClC chloride carriers as ion channels, as they are secondary active [[carriers]].<br /> <br /> == Weblinks ==<br /> *[http://www.tcdb.org/ The TCDB database]<br /> *[http://www.tcdb.org/tcdb/subclass2.php?tc=1.A TCDB: 1.A α-Type channels]<br /> *[http://www.tcdb.org/pdb_structure.php TCDB: Transport proteins with PDB structures]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930871 2009-02-21T16:41:52Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[User:Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)<br /> <br /> '''problems with scenes changing unexpectedly''' appear in the first applet on the [[aconitase]] page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different (the three yellow amino side chains around the cluster lack several atoms/bonds then). I have a problem with 3, too, as it doesn't show as it was saved, but this is more elusive at the moment. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930870 2009-02-21T16:37:03Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[User:Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)<br /> <br /> '''problems with scenes changing unexpectedly''' appear in the first applet on the [[aconitase]] page. There are 3 green links, and if you click 1,2,1,2,1... the two scenes will stay as they show the first time clicked, but as soon as you click 3, 2 will appear different. I have a problem with 3, too, as it doesn't show as it was saved but this is more elusive at the moment. --[[User:Ralf Stephan|Ralf Stephan]] 18:37, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930869 2009-02-21T16:20:38Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/4'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930868 2009-02-21T10:46:14Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */ try scripting</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/2'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:What%27s_New&diff=930867 2009-02-21T09:45:59Z

<p>Ralf Stephan: /* December, 2008 */ +Feb</p> <hr /> <div>&lt;big&gt;&lt;b&gt;What's New in Proteopedia?&lt;/b&gt;&lt;/big&gt;<br /> &lt;br&gt;<br /> This page lists new pages, substantially updated pages, and new capabilities '''within''' Proteopedia. In contrast, [[Proteopedia:News]] lists '''external''' news such as adoptions, blogs, press, meetings, seminars and workshops about Proteopedia.<br /> <br /> A major purpose of this page is to make it easier for users to find out about new user-created pages with substantial content. Only user-created pages that have substantial content (at least one paragraph of user-added text with three or more green links), and that are reasonably complete should be listed below. Pages that are started, but not yet completed, should not be listed until they are reasonably complete. Automatically seeded new pages, titled with PDB codes, are not listed here&lt;ref&gt;You can find new entries in the [[PDB]] by going to [http://www.rcsb.org RCSB] and searching by date range.&lt;/ref&gt;. Minor updates to existing pages should not be listed.<br /> &lt;div style='float: right; width: 50%;'&gt;<br /> &lt;br&gt;&lt;br&gt;<br /> &lt;br&gt;&lt;br&gt;<br /> &lt;br&gt;&lt;br&gt;<br /> &lt;br&gt;&lt;br&gt;<br /> Please add new items at the top. If a linked page is not new, but has been updated with substantial new content, please say so. Each page's ''history'' tab (at the top) shows when it was created and the date of each update.<br /> &lt;br&gt;&lt;br&gt;<br /> The left arrow symbol (&lt;-) signifies a page that [[Help:Editing#Redirecting_One_Page_to_Another_Page|redirects]] to another page.<br /> &lt;/div&gt;<br /> <br /> ==February, 2009==<br /> *[[Ion channels]] is an attempt to cover a family of proteins and list their available PDB structures<br /> <br /> ==December, 2008==<br /> *[[Conservation, Evolutionary]] now includes instructions on how to show a ConSurf result as a scene in Proteopedia, complete with the standard ConSurf color key.<br /> *[[Resolution]] now includes a movie illustrating the relation between the atomic model and the electron density map while resolution ranges from 0.5 to 5.0 &amp;Aring;ngstroms.<br /> <br /> ==November, 2008==<br /> *[[User:Wayne_Decatur/Suppression_of_RNA_Silencing_by_Viruses|RNA silencing: suppression by viruses]]. Concerns the research awarded the [http://nobelprize.org/nobel_prizes/medicine/laureates/2006/ 2006 Nobel Prize in Physiology or Medicine]. Linked are new pages on specific RNA silencing proteins: [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|Plant viral protein p19]] and [[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing|Tomato aspermy virus protein 2b]].<br /> *[[Transcription Termination Factor Rho]].<br /> *Mechanosensitive ion channel of large conductance, with open, intermediate, and closed conformations, [[2oar]].<br /> *Crucial role of electrostatic features in halotolerance of carbonic anhydrase, [[1y7w]].<br /> *[[Hydrogen in macromolecular models]]<br /> *[[Molecular modeling and visualization software]], whick links to new pages on [[PyMOL]], [[Jmol]], [[RasMol]], and [[Chime]].<br /> <br /> ==October, 2008==<br /> *[[Lac repressor]] structure, including a morph of the DNA-binding domain bending the operator DNA.<br /> *Poly(A) Polymerase, [[2q66]]: A new section complementing this month's article in [[Molecule of the Month]].<br /> *[[Structure Gallery Generator]] generates galleries of thumbnail molecular images, linked to Proteopedia, for external websites or within Proteopedia pages.<br /> *Acetylcholinesterase in complex with anti-Alzheimer's drug candidates: Crystal packing mediates enantioselective ligand recognition, [[1zgb]].<br /> *Thermal stability analysis of alcohol dehydrogenase: [[2oui]], [[2nvb]].<br /> *Confirmation of a heterodimer predicted by computational genomic analysis (neither chain could be crystallized alone): [[2g38]].<br /> *Complex Of ''S. griseus'' Proteinase B And Polypeptide Chymotrypsin Inhibitor-1 From Russet Burbank Potato Tubers, [[4sgb]].<br /> *''Structures Saving the Most Lives'' is a new list added to the [[Highest impact structures]] page originally created in February, 2008.<br /> *[[Hydrogen bonds]]<br /> *[[Nobel Prizes for 3D Molecular Structure]]<br /> *[[Morphs]]: Although this page was created in March, 2008, most of its content was added this month.<br /> *[[Proteopedia: Email list]]<br /> *[[Proteopedia:What's New|What's New in Proteopedia?]] (this page).<br /> *Several pages about visualization software: [[FirstGlance in Jmol]], [[Swiss-PDBViewer = DeepView]], and [[Protein Explorer]].<br /> <br /> ==September, 2008==<br /> *Anticancer Prodrug CPT-11 complexed with ''Torpedo californica'' Acetylcholinesterase [[1u65]]<br /> *[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]<br /> *Insecticidal delta-endotoxin [[Cyt2Ba]] from ''Bacillus thuringiensis''.<br /> *TEM1-β-Lactamase/ β-Lactamase Inhibitor Protein (BLIP), [[2b5r]] and [[1s0w]].<br /> *Acid-beta-glucosidase covalently bound to conduritol B epoxide, [[1y7v]].<br /> *Ribonuclease A, [[1rta]] has a new section complementing this month's article in [[Molecule of the Month]].<br /> *[[DRuMS]], standard color schemes for macromolecules, and color key templates for use in Proteopedia.<br /> *[[User:Tom Gluick/glutamine synthetase|Glutamine Synthetase]], which includes instructions on how to use the Jmol console for advanced scene authoring.<br /> <br /> ==August, 2008==<br /> *[[HIV-1 protease]]<br /> *[[Pyruvate phosphate dikinase]] with a morph of the catalytic reaction and conformational changes.<br /> *[[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]] with a morph of the catalytic reaction and conformational changes.<br /> *[[Antizyme Inhibitor]]<br /> *Selenocysteine Synthase, [[SelB Recognition]] is a new page complementing this month's article in [[Molecule of the Month]].<br /> *[[Teaching Strategies Using Proteopedia‎]]<br /> *[[User:J._Shaun_Lott/BIOSCI_203|Protein structure lesson plan for BioSci 203]]<br /> *[[Proteopedia: News]]<br /> <br /> ==July, 2008==<br /> *[[Biotin Protein Ligase]]<br /> *YAGE, A Prophage Protein Belonging To The Dihydrodipicolinic Acid Synthase Family From E. Coli K12, [[2v9d]].<br /> *[[User:Karl_Oberholser/Ramachandran_Plots|Ramachandran Plots]]<br /> *[[Flexibility of aromatic residues in acetylcholinesterase]]<br /> *Horizontal gene transfer ssDNA binding protein from ''Agrobacterium tumefaciens'' [[VirE1/VirE2]]=[[3btp]]<br /> *[[Proteopedia:Page of the Year Competition]]<br /> *[[Student Projects]]<br /> <br /> ==June 2008==<br /> *Computational design of a Kemp elimination catalyst [[2rkx]].<br /> *[[Recoverin, a calcium-activated myristoyl switch‎]]<br /> *G protein, ras oncogene: [[James_D_Watson/Proteins_Intro]].<br /> *[[Ribulose-1,5-bisphosphate carboxylase/oxygenase]] uses the Kinemage applet.<br /> *[[Acid-beta-glucosidase]]<br /> *[[Rop protein]]<br /> <br /> *[[Institute of Clinical Biochemistry]], Oslo, Norway.<br /> *[[Research Groups]] &lt;- [[Institutes]]<br /> *[[Teaching Scenes, Tutorials, and Educators' Pages‎]]<br /> <br /> <br /> '''About Macromolecular Structure'''<br /> *[[About Macromolecular Structure]] &lt;- [[About Protein Structure]]<br /> *[[Amino Acids]]<br /> *[[Asymmetric Unit]]<br /> *[[Atomic coordinate file]]<br /> *[[Biological Unit]] &lt;- [[Quaternary structure]]<br /> *[[Free R]]<br /> *[[NMR Ensembles of Models‎]]<br /> *[[PDB identification code]]<br /> *[[Quality assessment for molecular models]]<br /> *[[R value]]<br /> *[[Resolution]]<br /> *[[Temperature value]] &lt;- [[Disorder]], [[B value]]<br /> *[[Unit cell]]<br /> <br /> ==May 2008==<br /> *[[Acetylcholinesterase]]<br /> *[[2ace]] with an overview of the significance of this, the first acetylcholinesterase structure.<br /> *Anti-Alzheimer's drug, Aricept, complexed with acetylcholinesterase [[1eve]].<br /> *Tacrine Binding To Aromatic Residues In The Active-site Gorge Of Acetylcholinesterase, [[1acj]].<br /> *Serum Paraoxonase-1 (PON1) via directed evolution [[1v04]].<br /> *Human acid-beta-glucosidase, [[1ogs]].<br /> *[[Photosystem II]], an undergraduate project.<br /> *[[Ozonolysis]]: cool animation of a chemical reaction!<br /> <br /> *[[Help:Copying FirstGlance Scenes into Proteopedia]]<br /> <br /> ==April 2008==<br /> *Acetylcholinesterase inhibited by nerve agent soman [[1som]].<br /> *Highest resolution acetylcholinesterase so far, [[1ea5]].<br /> *Tetramerization domain of acetylcholinesterase [[1vzj]].<br /> *Locations of mutations in oncogene phosphatidylinositol 3-kinase [[2rd0]], with many of the published figures made interactive in Jmol.<br /> *Escherichia coli GlpG, an integral membrane protein rhomboid protease, unique in cleaving the transmembrane domains of other membrane proteins, [[2ic8]].<br /> *[[Major Histocompatibility Complex Class I]] (no Jmol yet)<br /> *[[Personal favorites]]<br /> *[[Believe It or Not!]]<br /> *[[Help:Protected Pages]]<br /> <br /> ==March 2008==<br /> *Conformational flexibility in the peripheral site of Torpedo californica acetylecholinesterase revealed by the complex structure with a bifunctional inhibitor, [[2cek]].<br /> *[[Proton Channels]]<br /> *[[Proteopedia:Namespaces]]<br /> *[[Proteopedia:About]]<br /> *[[SGAP]] Streptomyces griseus Aminopeptidase (SGAP) (''no Jmol'')<br /> <br /> ==February 2008==<br /> *[[Hemoglobin]]<br /> *[[Highest impact structures]] of all time.<br /> *[[Nucleosomes]]<br /> *Scorpion alpha-toxin [[1qlh]].<br /> *[[Peptide]]<br /> *[[Proteopedia:Problems]]<br /> *[[Personal favorites]]<br /> <br /> ==January 2008==<br /> *[[AChE inhibitors and substrates]]<br /> *[[Dihydrofolate reductase]]<br /> <br /> ==October-December 2007==<br /> *[[Serine Protease]]<br /> *[[Nqo1]] NADH quinone oxidoreductase (NQO1) in complex with its potent inhibitor dicoumarol.<br /> *[[1xjo]] ''S. griseus'' aminopeptidase.<br /> *[[Glycine]]<br /> *[[Bacterial Intein-Like Domains (BILs)]] (no Jmol, no green links)<br /> *[[Hint auto-proteolytic protein-processing domains]] (no Jmol, no green links)<br /> <br /> ==See Also==<br /> <br /> *[[Proteopedia:News]]<br /> *[[Proteopedia: Email list]]<br /> *[[Special:Newpages|Newest Pages]] appears to list only the current month, and mostly automatically seeded pages.<br /> *[[Special:Recentchanges|Most Recent Changes]]<br /> *[[Topic pages]]<br /> <br /> ==Notes==<br /> &lt;references /&gt;</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930866 2009-02-21T08:32:57Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[User:Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930865 2009-02-21T08:32:23Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */ disappearing references</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST) -- Thanks for finding this bug Ralf. Actually internal links were working in applet captions, but not in applet captions that specified an initial scene rather than the default view. Now fixed. --[[User:Eran Hodis|Eran Hodis]] 19:18, 18 February 2009 (IST)<br /> <br /> '''&lt;nowiki&gt;&lt;references /&gt;&lt;/nowiki&gt; disappear''' when placed ''after'' a second &lt;nowiki&gt;&lt;applet&gt;&lt;/nowiki&gt;, see a minimal test case at [[Ralf_Stephan/Sandbox_2]]. --[[User:Ralf Stephan|Ralf Stephan]] 10:32, 21 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=User:Ralf_Stephan/Sandbox_2&diff=930864 2009-02-21T08:28:40Z

<p>Ralf Stephan: test</p> <hr /> <div>&lt;applet load='1xyz' /&gt;<br /> '''Test''' &lt;ref&gt;Ref&lt;/ref&gt;<br /> &lt;applet load='1xyz' /&gt;<br /> &lt;references/&gt;</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930856 2009-02-20T17:05:12Z

<p>Ralf Stephan: /* References */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references/&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930855 2009-02-20T17:04:25Z

<p>Ralf Stephan: ref</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with tetrahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.&lt;ref&gt;PMID:8151704&lt;/ref&gt;<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == References ==<br /> &lt;references /&gt;<br /> <br /> == External links ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930854 2009-02-20T16:47:26Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;Both mAc and cAc are quite similar in their ACO function. Studies, however, concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. ACO is an excellent system for understanding the role of iron-sulfur-clusters in catalysis. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 &lt;scene name='Aconitase/7acn-sf4-3cys-solo/1'&gt;which are bound to three of the four&lt;/scene&gt; cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with terahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Weblinks ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930807 2009-02-20T16:18:49Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;The bulk of citrate cycle processing happens in mitochondria and so, studies concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451 which are bound to three of the four cluster iron atoms. The fourth, Fe4, is free to bind; it can be four-, five-, or six-coordinate, but is constrained to bond to three sulfur atoms of the (4Fe-4S)-cluster with terahedral geometry. Thus, Fe4 is free to bind one, two, or three partners, in this reaction always oxygen atoms belonging to other molecules. As Fe4 is not bound very fast to the cluster, it moves quite a bit around in the process of bonding and debonding.<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Weblinks ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=User_talk:Ralf_Stephan&diff=930484 2009-02-18T18:03:19Z

<p>Ralf Stephan: /* Internal links in Applet captions */</p> <hr /> <div>'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! [[User:Eran Hodis|Eran Hodis]] 14:14, 6 February 2009 (IST)<br /> <br /> == Morphs ==<br /> <br /> Hi Ralf,<br /> <br /> Eventually you might want to consider adding morphs to give the idea of the conformational changes in the transport proteins between their open and closed states. An example can be found on the [[Proton Channels]] page that Eric Martz created. The morph itself does not represent the actual motion between the two states -- open and closed -- but rather is a linear interpolation (in most morphs) between the starting structure and the ending structure.<br /> <br /> Best,<br /> [[User:Eran Hodis|Eran Hodis]] 18:37, 6 February 2009 (IST)<br /> <br /> :Yes, actually, I chose my first protein after I had a good look at the Yale gallery what they had. I'm aware of the scarcity of structures. Thanks. --[[User:Ralf Stephan|Ralf Stephan]] 18:41, 6 February 2009 (IST)<br /> <br /> <br /> ==Reponse==<br /> <br /> Hi Ralf, I responded on my user talk page. Best, --[[User:Eran Hodis|Eran Hodis]] 02:35, 8 February 2009 (IST)<br /> <br /> == Wikipedia link to Metalloproteases ==<br /> <br /> In regards to a Wikipedia link to the page on metalloproteases, please see [[Proteopedia:Policy#Links_to_Wikipedia]]. You're welcome to help shape this policy, but our current thinking is that if the link is to a page that could benefit from 3D images, then we should link to the page in Proteopedia (even if it doesn't exist, to encourage creation), and that page can then link to Wikipedia. --[[User:Eran Hodis|Eran Hodis]] 12:34, 8 February 2009 (IST)<br /> :No, you're right, the german language entry is much better. I'll translate it for Proteopedia. --[[User:Ralf Stephan|Ralf Stephan]] 12:36, 8 February 2009 (IST)<br /> <br /> == Gzipped PDBS ==<br /> <br /> You should now be able to upload gzipped PDBs --[[User:Eran Hodis|Eran Hodis]] 19:08, 17 February 2009 (IST)<br /> :Great, many thanks! --[[User:Ralf Stephan|Ralf Stephan]] 20:55, 17 February 2009 (IST)<br /> <br /> == Internal links in Applet captions ==<br /> <br /> Hi Ralf,<br /> Fixed this problem. Thanks for pointing out bugs that are simple to fix!<br /> --[[User:Eran Hodis|Eran Hodis]] 19:20, 18 February 2009 (IST)<br /> :Thanks for fixing, anyway! --[[User:Ralf Stephan|Ralf Stephan]] 20:03, 18 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930468 2009-02-18T17:01:46Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browser URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> '''Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt;''' don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Proteopedia:Problems&diff=930467 2009-02-18T17:00:13Z

<p>Ralf Stephan: /* Problems that can be fixed after widespread use begins */ two suggestions, one problem</p> <hr /> <div>This page is for listing problems in existing features. Please list desired new features on the page [[Proteopedia:Wishlist]]<br /> <br /> When a problem below has been fixed, please prefix it with &quot;Fixed (date):&quot;, rather than deleting it from this page. In this way everyone knows what problems have been fixed and when.<br /> <br /> ==Problems that need fixing before widespread announcement==<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Green links need to work in Firefox version 2, with Java version 1.60_03 and higher! --working on it --[[User:Eran Hodis|Eran Hodis]] 20:13, 12 April 2008 (IDT)<br /> <br /> '''Help: Searching''' needs to be revised to agree with the actual search behavior (which needs careful testing) and to explain the limitations and advantages (with examples) of the WikiMedia Search (as modified) vs. the Google search. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; (''Pages in the User namespace can now have Jmol Scenes'') Document that pages in the User: namespace cannot have Jmol scenes, or else enable that. It seems natural for users to put scenes on their personal pages. If it is to remain disabled, then the SAT should not be openable, and instead a message of explanation should appear where the SAT +/- normally is. [[User:Emartz|Emartz]] 20:50, 26 March 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; Searching for &quot;Sandbox&quot; fails to find either the page titled &quot;Sandbox&quot; or the page titled &quot;Sandbox 2&quot;. And searching for &quot;sandbox&quot; also fails, despite that word occuring in the text of each page! [[User:Emartz|Emartz]] 03:25, 26 March 2008 (IST) '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 26 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; The format of Jmol's '''hover report''' needs to be correct on all pages. Currently it is incorrect on the main page. [[User:Emartz|Emartz]] 02:38, 16 March 2008 (IST) '''''Solved''''' by [[User:EH| Eran]] 25 March 2008 -- let me know if problems with hover surface again<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Search result ordering:''' list pages that don't begin with a numeral before pages that do. Example: Search for &quot;mhc&quot;. The page &quot;Major histocompatibility complex class I&quot; appears almost at the end of the 400-some length list, curiously before 3c9n. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST). '''''Solved''''' by Anat Kats and [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Singular vs. plural in searches''': Searching for &quot;antigens&quot; fails to find &quot;Category:Histocompatibility_antigen&quot;, but searching for &quot;antigen&quot; finds it. Ideally, relevant pages should be found regardless of whether the query term is singular or plural. [[User:Emartz|Emartz]] 02:44, 16 March 2008 (IST). '''''Solved''''' by [[User:J Prilusky|J Prilusky]] 25 March 2008<br /> <br /> '''Jmol Extensions need to work.''' Example of non-working checkboxes: [[Nucleosomes#Scenes_for_Projection_in_Biochemistry_Classes]]. The checkboxes appear but checking them does not send the script to Jmol. I note this item concerning the installation of Jmol extensions:<br /> <br /> * Add the following line to the end of LocalSettings.php:<br /> * require_once('extensions/Jmol/Jmol.php');<br /> <br /> This is here under Installation:<br /> [http://wiki.jmol.org/index.php/MediaWiki wiki.jmol.org/index.php/MediaWiki] [[User:Emartz|Emartz]] 22:06, 28 February 2008 (IST)<br /> <br /> '''Namespace lists:''' ''PARTIALLY SOLVED, see [[Proteopedia:Namespaces]] but the links don't work.'' Need a way to list namespaces, and pages within each namespace. For example, see [http://en.wikipedia.org/wiki/Wikipedia:Namespace Wikipedia: Namespace]. Perhaps this should be an item on the the left, similar to &quot;Special Pages&quot;. I see no way to list the pages within a namespace (to find out what they are). The &quot;Special pages&quot; do not seem to include such lists. If I use the checkboxes on the search results page to limit a search to the Proteopedia namespace, and search for &quot;proteopedia&quot;, I get 4 hits (Troubleshooting, Policy, Wishlist, Problems). But there may be other pages in this namespace that don't explicitly mention the query term, which therefore will not appear on the search results list. Namespaces are rather important for authors to know about. That is why I think a way to list these pages is a high priority. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; ''On page [[1c96]], the ligand FLC (fluorocitrate?) is shown while, if you click on its green link, it's really a citrate. I don't know of other instances but I'll now look for them. --[[User:Ralf Stephan|Ralf Stephan]] 19:22, 15 February 2009 (IST) ♣ Ligand green links are generated from the PDB file. I checked the PDB file, and what is being displayed matches the PDB file. If this is really an error then please notify the PDB. They can fix the file, and we will update the page accordingly. --[[User:Eran Hodis|Eran Hodis]] 20:40, 15 February 2009 (IST) ♣ This is not really a problem. PDB (RCSB) is not required to name ligands and short molecules following any known nomenclature. In the structure file for 1c96 you may find this line: ''HETNAM FLC CITRATE ANION'' from where [[User:OCA|OCA]] gets the name for Proteopedia. Other interesting example can be found in structure 1yuh, featuring Np, the official symbol for Neptunium to indicate 3-nitropropanoic acid. [[User:Jaime_Prilusky|Jaime Prilusky]] Sun Feb 15 22:01:33 IST 2009<br /> <br /> == Problems that can be fixed after widespread use begins==<br /> <br /> '''Category: singular vs. plural:''' Category:Nucleosome and Category:Nucleosomes are two separate pages with nonoverlapping contents. It would be great if all pairs of the same term +/- a terminal &quot;s&quot; can be merged into a single page per such pair. [[User:Emartz|Emartz]] 19:32, 28 February 2008 (IST)<br /> :As this is a pressing problem that only can be gotten right with human intervention, I'd suggest at least a user-editable synonyms list that contains such many-to-one relationships---a sort of dictionary, if you will, that is used '''before''' finally applying a category to a PDB. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Search result ordering:''' Perhaps PDB code-titled pages should be ordered to show those with the most hits of the search term above those with fewer hits? [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> <br /> '''Special pages &amp;gt; Categories:''' This very long list needs a mechanism to jump to a letter of the alphabet. Otherwise, it is unusable because it has tens of thousands of items. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> :Until we have the alphabet, there is a workaround, see my user page, where I have three such searches edited to my liking. You can do that too, just by editing such a link in your browse URL line. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)<br /> <br /> '''Scene tags placed in a bulleted list''' don't display as green links. [[User:Emartz|Emartz]] 17:36, 28 February 2008 (IST)<br /> &lt;u&gt;&lt;i&gt;Workaround&lt;/i&gt;&lt;/u&gt;: Use standard bullet list HTML notation instead of wikitext markup [[User:J Prilusky|J Prilusky]] 9:11 3 March 2008<br /> <br /> '''Scenes that have green displayed text that includes non-alphabetical characters like ampersands and greek letters''' do not display properly --[[User:Eran Hodis|Eran Hodis]] 17:24, 12 June 2008 (IDT)<br /> <br /> '''Models with &gt;100,000 atoms''' fail to display due to java memory limitations. These are &lt;0.1% of the PDB. I suggest that a box be inserted automatically (from a template) on such pages that explains why Jmol remains blank. We should test whether increasing the memory allocated to java reduces this problem, and if so, provide an explanation of how to increase java memory in Win and OS X. See also [http://bioportal.weizmann.ac.il/oca-docs/fgij/bigpdb.htm tests with big PDB files] and a [http://bip.weizmann.ac.il/oca-docs/PDBRecNamStats/PDBSizeDistribution.html list of the largest files in the PDB]. [[User:Eric Martz|Eric Martz]] 19:20, 13 April 2008 (IDT)<br /> <br /> '''Green (initial scene) link in structure box''' should recall the user specified initial scene rather than the default Proteopedia initial scene --[[User:Eran Hodis|Eran Hodis]] 16:20, 17 June 2008 (IDT)<br /> <br /> &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED'''&lt;/span&gt; '''Gzipped PDBs''' should be accepted since Jmol accepts them as they are. I have here a 11,5 MB morph that when gzipped is only 2,8 MB. I don't want to upload nor download four times the amount for no reason. --[[User:Ralf Stephan|Ralf Stephan]] 11:38, 17 February 2009 (IST) <br /> : You should now be able to upload gzipped PDBs. --[[User:Eran Hodis|Eran Hodis]] 19:07, 17 February 2009 (IST)<br /> <br /> Internal &lt;nowiki&gt;[[links]]&lt;/nowiki&gt; don't work when in an applet text string. --[[User:Ralf Stephan|Ralf Stephan]] 19:00, 18 February 2009 (IST)</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930454 2009-02-18T16:45:41Z

<p>Ralf Stephan: /* Catalytic mechanism of mitochondrial ACO */</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;The bulk of citrate cycle processing happens in mitochondria and so, studies concentrated on &lt;scene name='Aconitase/7acn-sf4/1'&gt;the mitochondrial ACO&lt;/scene&gt;. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451.<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Weblinks ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan https://proteopedia.org/index.php?title=Aconitase&diff=930453 2009-02-18T16:34:34Z

<p>Ralf Stephan: catalytic applet, two scenes</p> <hr /> <div>'''Aconitase (ACO)''' is an enzymatic domain that confers the ability to catalyse the equilibrium<br /> :citrate = aconitate + H&lt;sub&gt;2&lt;/sub&gt;O = L-isocitrate<br /> This reaction is part of the citrate (TCA-, Krebs-)cycle.<br /> <br /> In most organims, there is a cytosolic enzyme with an ACO domain (cAc), and in eukaryotes, a second copy of it was introduced with mitochondria (mAc). Plants developed even more copies in mitochondria.<br /> <br /> == Catalytic mechanism of mitochondrial ACO ==<br /> &lt;applet load=7acn scene='Aconitase/7acn-sf4/1' size='400' frame='true' align='left' caption=&quot;Mitochondrial aconitase from pig, PDB [[7acn]].&quot; /&gt;The bulk of citrate cycle processing happens in mitochondria and so, studies concentrated on the mitochondrial ACO. The &lt;scene name='Aconitase/7acn-sf4-3cys/1'&gt;(4Fe-4S) cofactor is held in place&lt;/scene&gt; by three sulfur atoms belonging to the cysteins-385, -448, and -451.<br /> <br /> &lt;!--It is clear that, in order to synthesize L-isocitrate, stereoselective catalysis must occur.--&gt;<br /> <br /> == Cytosolic aconitase and its other function ==<br /> &lt;applet load='Morph_2ipy-2b3x.pdb.gz' scene='Aconitase/2ipy-total/2' size='400' frame='true' align='right' caption=&quot;Cytosolic aconitase from rabbit (bound to RNA) and human (with Fe4S4 cluster), from PDB [[2ipy]] and [[2b3x]].&quot; /&gt;A specialty of cAc is that in mammals it has developed a &lt;scene name='Aconitase/2ipy-total/2'&gt;second function&lt;/scene&gt; as inhibitor of &lt;scene name='Aconitase/2ipy-rna/1'&gt;those mRNA&lt;/scene&gt; that carry an &lt;scene name='Aconitase/2ipy-rna-ire/1'&gt;iron-responsive element (IRE)&lt;/scene&gt;. Therefore, the cytosolic cAc is named IREBP for IRE-binding protein when this function is talked about. Only one of the two functions is active, depending on whether &lt;scene name='Aconitase/2b3x-cluster/1'&gt;the (4Fe-4S) cofactor&lt;/scene&gt; is present in the molecule: it's essential for &lt;scene name='Aconitase/2b3x-total/1'&gt;the ACO function&lt;/scene&gt;. You can see, by &lt;scene name='Aconitase/Morph/2'&gt;looking at the morph&lt;/scene&gt;, how much the enzyme structure differs between those two functions.<br /> <br /> &lt;!--== Available structures ==<br /> In the PDB, nearly all deposited structures are from mammals, [[1l5j]] is from ''E.coli''. Also, only [[2ipy]] shows the IREBP function of cAc---it's also the only from rabbit. There are only two other cAc structures, with and without citrate, also the only from human. All other structures are either cow or pig, and a mutant from pig; all three proteins with several different ligands and inhibitors.<br /> <br /> *[[1aco]] - mAc (''Bos taurus'') with ''trans''-aconitate (inhibitor)<br /> *[[1ami]] - mAc (''Bos taurus'') with methylisocitrate<br /> *[[1amj]] - mAc (''Bos taurus'') with sulfate and hydroxide<br /> *[[1b0j]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate (substrate)<br /> *[[1b0k]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor)<br /> *[[1b0m]] - S642 mutant of mAc (''Sus scrofa'') with fluorocitrate (inhibitor) and oxygen<br /> *[[1c96]] - S642 mutant of mAc (''Sus scrofa'') with citrate<br /> *[[1c97]] - S642 mutant of mAc (''Sus scrofa'') with isocitrate and oxygen<br /> *[[1fgh]] - mAc (''Bos taurus'') with 4-hydroxy-''trans''-aconitate (inhibitor)<br /> *[[1l5j]] - aconitase B (''E. coli'') with Fe3S4 and aconitate<br /> *[[1nis]] - mAc (''Bos taurus'') with nitrocitrate (inhibitor)<br /> *[[1nit]] - mAc (''Bos taurus'') with sulfate<br /> *[[2b3x]] - cAc (human) as aconitase with Fe4S4<br /> *[[2b3y]] - cAc (human) as aconitase with Fe4S4 and citrate<br /> *[[2ipy]] - cAc (''Oryctolagus cuniculus'') as IRP1 with ferritin RNA<br /> *[[5acn]] - mAc (''Sus scrofa'') with Fe3S4 (missing a Fe)<br /> *[[6acn]] - mAc (''Sus scrofa'') with tricarballylic acid<br /> *[[7acn]] - mAc (''Sus scrofa'') with isocitrate<br /> *[[8acn]] - mAc (''Sus scrofa'') with nitroisocitrate<br /> --&gt;<br /> == Weblinks ==<br /> *[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Molecule of the Month: Aconitase and Iron Regulatory Protein 1]<br /> *[http://en.wikipedia.org/wiki/Aconitase Aconitase at Wikipedia]</div>

Ralf Stephan