1o8c

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Current revision

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

Structural highlights

1o8c is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ACUI_ECOLI Probably catalyzes the NADPH-dependent reduction of acrylyl-CoA to propanoyl-CoA.^[1]

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

As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The overall fold of YhdH is very similar to that of alcohol dehydrogenases and quinone reductases despite its low sequence identity. The absence of any Zn ion indicates that YdhH is a putative quinone oxidoreductase. YhdH forms a homodimer, with each subunit composed of two domains: a catalytic domain and a coenzyme-binding domain. NADP is bound in a deep cleft formed between the two domains. Large conformational changes occur upon NADP binding, with the two domains closing up to each other and narrowing the NADP-binding cleft. Comparisons of the YdhH active site with those of the quinone oxidoreductases from Escherichia coli and Thermus thermophilus made it possible to identify essential conserved residues as being Asn41, Asp43, Asp64 and Arg318. The active-site size is very narrow and unless an induced fit occurs is accessible only to reagents the size of benzoquinone.

Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.,Sulzenbacher G, Roig-Zamboni V, Pagot F, Grisel S, Salomoni A, Valencia C, Campanacci V, Vincentelli R, Tegoni M, Eklund H, Cambillau C Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1855-62. Epub 2004, Sep 23. PMID:15388933^[2]

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

References

↑ Todd JD, Curson AR, Sullivan MJ, Kirkwood M, Johnston AW. The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate. PLoS One. 2012;7(4):e35947. doi: 10.1371/journal.pone.0035947. Epub 2012 Apr 26. PMID:22563425 doi:http://dx.doi.org/10.1371/journal.pone.0035947
↑ Sulzenbacher G, Roig-Zamboni V, Pagot F, Grisel S, Salomoni A, Valencia C, Campanacci V, Vincentelli R, Tegoni M, Eklund H, Cambillau C. Structure of Escherichia coli YhdH, a putative quinone oxidoreductase. Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1855-62. Epub 2004, Sep 23. PMID:15388933 doi:10.1107/S0907444904020220

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/1o8c"

@@ Line 3: / Line 3: @@
 <StructureSection load='1o8c' size='340' side='right'caption='[[1o8c]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1o8c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O8C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1o8c]] is a 4 chain structure with sequence from [https://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=1O8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O8C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1o89|1o89]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></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=1o8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o8c OCA], [https://pdbe.org/1o8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o8c RCSB], [https://www.ebi.ac.uk/pdbsum/1o8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o8c ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACUI_ECOLI ACUI_ECOLI] Probably catalyzes the NADPH-dependent reduction of acrylyl-CoA to propanoyl-CoA.<ref>PMID:22563425</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Bignon, C]]
+[[Category: Bignon C]]
-[[Category: Cambillau, C]]
+[[Category: Cambillau C]]
-[[Category: Grisel, S]]
+[[Category: Grisel S]]
-[[Category: Pagot, F]]
+[[Category: Pagot F]]
-[[Category: Roig-Zamboni, V]]
+[[Category: Roig-Zamboni V]]
-[[Category: Salamoni, A]]
+[[Category: Salamoni A]]
-[[Category: Sulzenbacher, G]]
+[[Category: Sulzenbacher G]]
-[[Category: Tegoni, M]]
+[[Category: Tegoni M]]
-[[Category: Valencia, C]]
+[[Category: Valencia C]]
-[[Category: Vincentelli, R]]
+[[Category: Vincentelli R]]
-[[Category: Possible nadph-dependent quinone oxidoreductase]]
-[[Category: Structural genomic]]
-[[Category: Unknown function]]

1o8c

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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