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==Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid== | ==Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid== | ||
<StructureSection load='3kb6' size='340' side='right' caption='[[3kb6]], [[Resolution|resolution]] 2.12Å' scene=''> | <StructureSection load='3kb6' size='340' side='right'caption='[[3kb6]], [[Resolution|resolution]] 2.12Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3kb6]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3kb6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pi1 2pi1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KB6 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.12Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene></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=3kb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kb6 OCA], [https://pdbe.org/3kb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kb6 RCSB], [https://www.ebi.ac.uk/pdbsum/3kb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kb6 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/O66939_AQUAE O66939_AQUAE] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/3kb6_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/3kb6_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 30: | Line 31: | ||
==See Also== | ==See Also== | ||
*[[Lactate | *[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Aquifex aeolicus | [[Category: Aquifex aeolicus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Antonyuk | [[Category: Antonyuk SV]] | ||
[[Category: Bessho | [[Category: Bessho Y]] | ||
[[Category: Ellis | [[Category: Ellis MJ]] | ||
[[Category: Hasnain | [[Category: Hasnain SS]] | ||
[[Category: Kuramitsu | [[Category: Kuramitsu S]] | ||
[[Category: Strange RW]] | |||
[[Category: Strange | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | |||
Latest revision as of 19:10, 1 November 2023
Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acidCrystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structure of D-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 A. The structure was solved by molecular replacement using the coenzyme-binding domain of Lactobacillus helveticus D-lactate dehydrogenase and contained two homodimers in the asymmetric unit. Each subunit of the homodimer was found to be in a ;closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft. Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).,Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt, 12):1209-13. Epub 2009 Nov 27. PMID:20054113[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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