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.

1wnb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 02:06, 11 September 2015

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)

Structural highlights

1wnb is a 4 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1wnd
Activity:	Betaine-aldehyde dehydrogenase, with EC number 1.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[ABDH_ECOLI] Catalyzes the oxidation of 1-pyrroline, which is spontaneously formed from 4-aminobutanal, leading to 4-aminobutanoate (GABA). Can also oxidize n-alkyl medium-chain aldehydes, but with a lower catalytic efficiency.^[1] ^[2]

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

In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2.1.8), catalysing the oxidation of betaine aldehyde into glycine betaine. The structure of YdcW resembles that of other aldehyde dehydrogenases: it is tetrameric and binds a NADH molecule in each monomer. The NADH molecules, bound in the active site by soaking, are revealed to be in the "hydrolysis position". Activities experiments demonstrate that YdcW is more active on medium-chains aldehyde than on betaine aldehyde. However, soaking of betaine into YdcW crystals revealed its presence in one of the subunits, in two positions, a putative resting position and a hydride transfer ready position. Analysis of kinetics data and of the active site shape suggest an optimum binding of n-alkyl aldehydes up to seven to eight carbon atoms, possibly followed by a bulky cyclic or aromatic group.

Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase.,Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C J Mol Biol. 2004 Oct 8;343(1):29-41. PMID:15381418^[3]

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

References

↑ Samsonova NN, Smirnov SV, Novikova AE, Ptitsyn LR. Identification of Escherichia coli K12 YdcW protein as a gamma-aminobutyraldehyde dehydrogenase. FEBS Lett. 2005 Aug 1;579(19):4107-12. PMID:16023116 doi:http://dx.doi.org/S0014-5793(05)00775-1
↑ Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J Mol Biol. 2004 Oct 8;343(1):29-41. PMID:15381418 doi:10.1016/j.jmb.2004.08.030
↑ Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C. Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J Mol Biol. 2004 Oct 8;343(1):29-41. PMID:15381418 doi:10.1016/j.jmb.2004.08.030

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/1wnb"

@@ Line 2: / Line 2: @@
 <StructureSection load='1wnb' size='340' side='right' caption='[[1wnb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wnb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wnb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNB FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTL:BETAINE+ALDEHYDE'>BTL</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wnd|1wnd]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Betaine-aldehyde_dehydrogenase Betaine-aldehyde dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.8 1.2.1.8] </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=1wnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wnb RCSB], [http://www.ebi.ac.uk/pdbsum/1wnb 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=1wnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnb OCA], [http://pdbe.org/1wnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wnb RCSB], [http://www.ebi.ac.uk/pdbsum/1wnb PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1wnb" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[Category: Betaine-aldehyde dehydrogenase]]
-[[Category: Escherichia coli k-12]]
+[[Category: Ecoli]]
 [[Category: Cambillau, C]]
 [[Category: Gruez, A]]

1wnb

From Proteopedia

Revision as of 02:06, 11 September 2015

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)

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