1x0l: Difference between revisions

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<StructureSection load='1x0l' size='340' side='right'caption='[[1x0l]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='1x0l' size='340' side='right'caption='[[1x0l]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1x0l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X0L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1X0L FirstGlance]. <br>
<table><tr><td colspan='2'>[[1x0l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X0L FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hicdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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]] 1.85&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Homoisocitrate_dehydrogenase Homoisocitrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.87 1.1.1.87] </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=1x0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x0l OCA], [https://pdbe.org/1x0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x0l RCSB], [https://www.ebi.ac.uk/pdbsum/1x0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x0l ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1x0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x0l OCA], [http://pdbe.org/1x0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x0l RCSB], [http://www.ebi.ac.uk/pdbsum/1x0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1x0l ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HICDH_THET2 HICDH_THET2] Catalyzes the NAD(+)-dependent conversion of homoisocitrate to alpha-ketoadipate. In addition, has high activity with citrate, but is inactive with 3-isopropylmalate.<ref>PMID:12427751</ref> <ref>PMID:20735360</ref>
== 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=1x0l 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=1x0l ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of homoisocitrate dehydrogenase involved in lysine biosynthesis from Thermus thermophilus (TtHICDH) was determined at 1.85-A resolution. Arg85, which was shown to be a determinant for substrate specificity in our previous study, is positioned close to the putative substrate binding site and interacts with Glu122. Glu122 is highly conserved in the equivalent position in the primary sequence of ICDH and archaeal 3-isopropylmalate dehydrogenase (IPMDH) but interacts with main- and side-chain atoms in the same domain in those paralogs. In addition, a conserved Tyr residue (Tyr125 in TtHICDH) which extends its side chain toward a substrate and thus has a catalytic function in the related beta-decarboxylating dehydrogenases, is flipped out of the substrate-binding site. These results suggest the possibility that the conformation of the region containing Glu122-Tyr125 is changed upon substrate binding in TtHICDH. The crystal structure of TtHICDH also reveals that the arm region is involved in tetramer formation via hydrophobic interactions and might be responsible for the high thermotolerance. Mutation of Val135, located in the dimer-dimer interface and involved in the hydrophobic interaction, to Met alters the enzyme to a dimer (probably due to steric perturbation) and markedly decreases the thermal inactivation temperature. Both the crystal structure and the mutation analysis indicate that tetramer formation is involved in the extremely high thermotolerance of TtHICDH.
Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance.,Miyazaki J, Asada K, Fushinobu S, Kuzuyama T, Nishiyama M J Bacteriol. 2005 Oct;187(19):6779-88. PMID:16166541<ref>PMID:16166541</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1x0l" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
[[Category: Homoisocitrate dehydrogenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Asada, K]]
[[Category: Thermus thermophilus]]
[[Category: Fushinobu, S]]
[[Category: Asada K]]
[[Category: Kuzuyama, T]]
[[Category: Fushinobu S]]
[[Category: Miyazaki, J]]
[[Category: Kuzuyama T]]
[[Category: Nishiyama, M]]
[[Category: Miyazaki J]]
[[Category: Decarboxylating dehydrogenase]]
[[Category: Nishiyama M]]
[[Category: Lysine biosynthesis]]
[[Category: Oxidoreductase]]

Latest revision as of 13:35, 13 March 2024

Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus

1x0l, resolution 1.85Å

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