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.

2ez9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:31, 18 October 2017

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate

Structural highlights

2ez9 is a 2 chain structure with sequence from "lactobacillus_arabinosus"_fred_et_al. "lactobacillus arabinosus" fred et al.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1pow, 1pox, 1y9d, 2ez4, 2ez8, 2ezt, 2ezu
Gene:	pox5 ("Lactobacillus arabinosus" Fred et al.)
Activity:	Pyruvate oxidase, with EC number 1.2.3.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POXB_LACPL] Important for the aerobic growth. Decarboxylates pyruvate in four steps. The energy released is partially stored in acetyl phosphate.

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

Enzymes that use the cofactor thiamin diphosphate (ThDP, 1), the biologically active form of vitamin B(1), are involved in numerous metabolic pathways in all organisms. Although a theory of the cofactor's underlying reaction mechanism has been established over the last five decades, the three-dimensional structures of most major reaction intermediates of ThDP enzymes have remained elusive. Here, we report the X-ray structures of key intermediates in the oxidative decarboxylation of pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP- and flavin-dependent enzyme pyruvate oxidase (POX)3 from Lactobacillus plantarum. The structures of 2-lactyl-ThDP (LThDP, 2) and its stable phosphonate analog, of 2-hydroxyethyl-ThDP (HEThDP, 3) enamine and of 2-acetyl-ThDP (AcThDP, 4; all shown bound to the enzyme's active site) provide profound insights into the chemical mechanisms and the stereochemical course of thiamin catalysis. These snapshots also suggest a mechanism for a phosphate-linked acyl transfer coupled to electron transfer in a radical reaction of pyruvate oxidase.

The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.,Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:16680160^[1]

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

References

↑ Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R, Tittmann K. The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat Chem Biol. 2006 Jun;2(6):324-8. Epub 2006 May 7. PMID:16680160 doi:http://dx.doi.org/10.1038/nchembio788

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ez9"

@@ Line 1: / Line 1: @@
 ==Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate==
 <StructureSection load='2ez9' size='340' side='right' caption='[[2ez9]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pox5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1590 "Lactobacillus arabinosus" Fred et al.])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </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=2ez9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ez9 OCA], [http://pdbe.org/2ez9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ez9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ez9 PDBsum]</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=2ez9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ez9 OCA], [http://pdbe.org/2ez9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ez9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ez9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ez9 ProSAT]</span></td></tr>
 </table>
 == Function ==

2ez9

From Proteopedia

Revision as of 07:31, 18 October 2017

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox