3kb6: Difference between revisions

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{{Seed}}
[[Image:3kb6.png|left|200px]]


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==Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid==
The line below this paragraph, containing "STRUCTURE_3kb6", creates the "Structure Box" on the page.
<StructureSection load='3kb6' size='340' side='right'caption='[[3kb6]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
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<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>
{{STRUCTURE_3kb6|  PDB=3kb6  |  SCENE=  }}
<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>
</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>
    <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/main_output.php?pdb_ID=3kb6 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.


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


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3kb6" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_20054113}}, adds the Publication Abstract to the page
*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 20054113 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20054113}}
__TOC__
 
</StructureSection>
==About this Structure==
3KB6 is a 4 chains structure with sequences 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].
 
==Reference==
<ref group="xtra">PMID:20054113</ref><references group="xtra"/>
[[Category: Aquifex aeolicus]]
[[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: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[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: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 16:07:06 2010''

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

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:, , , , , ,
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.

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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