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[[Image:3kb6.png|left|200px]]
==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=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3kb6]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KB6 FirstGlance]. <br>
</td></tr><tr><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><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr><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])</td></tr>
<tr><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><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://www.rcsb.org/pdb/explore.do?structureId=3kb6 RCSB], [http://www.ebi.ac.uk/pdbsum/3kb6 PDBsum]</span></td></tr>
<table>
== 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>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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_3kb6|  PDB=3kb6  |  SCENE=  }}
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<ref>PMID:20054113</ref>


===Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_20054113}}
 
==About this Structure==
[[3kb6]] is a 4 chain structure with sequence from [http://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].


==See Also==
==See Also==
*[[Lactate Dehydrogenase|Lactate Dehydrogenase]]
*[[Lactate Dehydrogenase|Lactate Dehydrogenase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020054113</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[Category: D-lactate dehydrogenase]]
[[Category: D-lactate dehydrogenase]]

Revision as of 16:30, 29 September 2014

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

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.
Ligands:, , , , ,
NonStd Res:
Gene:aq_727, ldhA (Aquifex aeolicus)
Activity:D-lactate dehydrogenase, with EC number 1.1.1.28
Resources:FirstGlance, OCA, RCSB, PDBsum

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.

See Also

References

  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

3kb6, resolution 2.12Å

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