3kb6: Difference between revisions

Latest revision as of 16:10, 1 November 2023

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid

Structural highlights

3kb6 is a 4 chain structure with sequence from Aquifex aeolicus. This structure supersedes the now removed PDB entry 2pi1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.12Å
Ligands:	1PE, GOL, LAC, MSE, NAD, PEG, PPI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O66939_AQUAE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The 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.

References

↑ Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS. Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt, 12):1209-13. Epub 2009 Nov 27. PMID:20054113 doi:10.1107/S1744309109044935

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Antonyuk SV, Strange RW, Ellis MJ, Bessho Y, Kuramitsu S, Inoue Y, Yokoyama S, Hasnain SS. Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt, 12):1209-13. Epub 2009 Nov 27. PMID:20054113 doi:10.1107/S1744309109044935

[1]

@@ Line 1: / Line 1: @@
 ==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]] 2.12&Aring;' scene=''>
+<StructureSection load='3kb6' size='340' side='right'caption='[[3kb6]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kb6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KB6 FirstGlance]. <br>
+<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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.12&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_727, ldhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-lactate_dehydrogenase D-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.28 1.1.1.28] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kb6 OCA], [http://pdbe.org/3kb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kb6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kb6 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66939_AQUAE O66939_AQUAE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <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>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3kb6" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aquifex aeolicus huber and stetter 2001]]
+[[Category: Aquifex aeolicus]]
-[[Category: D-lactate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Antonyuk, S V]]
+[[Category: Antonyuk SV]]
-[[Category: Bessho, Y]]
+[[Category: Bessho Y]]
-[[Category: Ellis, M J]]
+[[Category: Ellis MJ]]
-[[Category: Hasnain, S S]]
+[[Category: Hasnain SS]]
-[[Category: Kuramitsu, S]]
+[[Category: Kuramitsu S]]
-[[Category: Structural genomic]]
+[[Category: Strange RW]]
-[[Category: Strange, R W]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: D-ldh]]
-[[Category: Nad]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Oxidoreductase]]
-[[Category: Rsgi]]

3kb6: Difference between revisions

Latest revision as of 16:10, 1 November 2023

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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