This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2pda

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:44, 9 March 2022

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.

Structural highlights

2pda is a 2 chain structure with sequence from Desulfovibrio africanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Activity:	Pyruvate synthase, with EC number 1.2.7.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[P94692_DESAF] Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity).[PIRNR:PIRNR000159]

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

Oxidative decarboxylation of pyruvate to form acetyl-coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR). Thus, PFOR is a potential target for drug design against certain anaerobic pathogens. Here, we report the crystal structures of the homodimeric Desulfovibrio africanus PFOR (data to 2.3 A resolution), and of its complex with pyruvate (3.0 A resolution). The structures show that each subunit consists of seven domains, one of which affords protection against oxygen. The thiamin pyrophosphate (TPP) cofactor and the three [4Fe-4S] clusters are suitably arranged to provide a plausible electron transfer pathway. In addition, the PFOR-pyruvate complex structure shows the noncovalent fixation of the substrate before the catalytic reaction.

Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.,Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC Nat Struct Biol. 1999 Feb;6(2):182-90. PMID:10048931^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Chabriere E, Charon MH, Volbeda A, Pieulle L, Hatchikian EC, Fontecilla-Camps JC. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Biol. 1999 Feb;6(2):182-90. PMID:10048931 doi:10.1038/5870

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pda"

@@ Line 3: / Line 3: @@
 <StructureSection load='2pda' size='340' side='right'caption='[[2pda]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pda]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PDA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PDA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pda]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PDA FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_synthase Pyruvate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.1 1.2.7.1] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_synthase Pyruvate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.1 1.2.7.1] </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=2pda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pda OCA], [http://pdbe.org/2pda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pda RCSB], [http://www.ebi.ac.uk/pdbsum/2pda PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pda ProSAT]</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=2pda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pda OCA], [https://pdbe.org/2pda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pda RCSB], [https://www.ebi.ac.uk/pdbsum/2pda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pda ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/P94692_DESAF P94692_DESAF]] Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity).[PIRNR:PIRNR000159]
+[[https://www.uniprot.org/uniprot/P94692_DESAF P94692_DESAF]] Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin (By similarity).[PIRNR:PIRNR000159]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2pda

From Proteopedia

Revision as of 07:44, 9 March 2022

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS AND PYRUVATE.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox