1jcl: Difference between revisions

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<StructureSection load='1jcl' size='340' side='right'caption='[[1jcl]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
<StructureSection load='1jcl' size='340' side='right'caption='[[1jcl]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JCL FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JCL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jcj|1jcj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jcl OCA], [https://pdbe.org/1jcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jcl RCSB], [https://www.ebi.ac.uk/pdbsum/1jcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jcl ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jcl OCA], [https://pdbe.org/1jcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jcl RCSB], [https://www.ebi.ac.uk/pdbsum/1jcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jcl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DEOC_ECOLI DEOC_ECOLI]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00592]  
[https://www.uniprot.org/uniprot/DEOC_ECOLI DEOC_ECOLI] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00592]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jcl ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jcl ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.
Observation of covalent intermediates in an enzyme mechanism at atomic resolution.,Heine A, DeSantis G, Luz JG, Mitchell M, Wong CH, Wilson IA Science. 2001 Oct 12;294(5541):369-74. PMID:11598300<ref>PMID:11598300</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jcl" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aldolase 3D structures|Aldolase 3D structures]]
*[[Aldolase 3D structures|Aldolase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Deoxyribose-phosphate aldolase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: DeSantis, G]]
[[Category: DeSantis G]]
[[Category: Heine, A]]
[[Category: Heine A]]
[[Category: Luz, J G]]
[[Category: Luz JG]]
[[Category: Mitchell, M]]
[[Category: Mitchell M]]
[[Category: Wilson, I A]]
[[Category: Wilson IA]]
[[Category: Wong, C H]]
[[Category: Wong C-H]]
[[Category: Alpha-beta tim barrel]]
[[Category: Lyase]]
Retrieved from "https://proteopedia.org/1jcl"