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| | <StructureSection load='1s20' size='340' side='right'caption='[[1s20]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='1s20' size='340' side='right'caption='[[1s20]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1s20]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S20 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S20 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1s20]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S20 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nxu|1nxu]]</div></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=1s20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s20 OCA], [https://pdbe.org/1s20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s20 RCSB], [https://www.ebi.ac.uk/pdbsum/1s20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s20 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YIAK, B3575 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1s20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s20 OCA], [http://pdbe.org/1s20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s20 RCSB], [http://www.ebi.ac.uk/pdbsum/1s20 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s20 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DLGD_ECOLI DLGD_ECOLI]] Catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate.<ref>PMID:11741871</ref> | + | [https://www.uniprot.org/uniprot/DLGD_ECOLI DLGD_ECOLI] Catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate.<ref>PMID:11741871</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Acton, T B]] | + | [[Category: Acton TB]] |
| - | [[Category: Benach, J]] | + | [[Category: Benach J]] |
| - | [[Category: Forouhar, F]] | + | [[Category: Forouhar F]] |
| - | [[Category: Kulkarni, K]] | + | [[Category: Kulkarni K]] |
| - | [[Category: Lee, I]] | + | [[Category: Lee I]] |
| - | [[Category: Montelione, G T]] | + | [[Category: Montelione GT]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Tong L]] |
| - | [[Category: Tong, L]] | + | [[Category: Xiao R]] |
| - | [[Category: Xiao, R]] | + | |
| - | [[Category: Alpha beta dimeric protein]]
| + | |
| - | [[Category: Nesg]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| Structural highlights
Function
DLGD_ECOLI Catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH, to form 3-keto-L-gulonate.[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
Escherichia coli YiaK catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH. It belongs to a large family of oxidoreductases that is conserved in archaea, bacteria, and eukaryotes but shows no sequence homology to other proteins. We report here the crystal structures at up to 2.0-A resolution of YiaK alone and in complex with NAD-tartrate. YiaK has a new polypeptide backbone fold and a novel mode of recognizing the NAD cofactor. In addition, NAD is bound in an unusual conformation, at the interface of a dimer of the enzyme. The crystallographic analysis unexpectedly revealed the binding of tartrate in the active site. Enzyme kinetics studies confirm that tartrate and the related D-malate are inhibitors of YiaK. In contrast to most other enzymes where substrate binding produces a more closed conformation, the binding of NAD-tartrate to YiaK produces a more open active site. The free enzyme conformation is incompatible with NAD binding. His(44) is likely the catalytic residue of the enzyme.
A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK).,Forouhar F, Lee I, Benach J, Kulkarni K, Xiao R, Acton TB, Montelione GT, Tong L J Biol Chem. 2004 Mar 26;279(13):13148-55. Epub 2004 Jan 12. PMID:14718529[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yew WS, Gerlt JA. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. J Bacteriol. 2002 Jan;184(1):302-6. PMID:11741871
- ↑ Forouhar F, Lee I, Benach J, Kulkarni K, Xiao R, Acton TB, Montelione GT, Tong L. A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK). J Biol Chem. 2004 Mar 26;279(13):13148-55. Epub 2004 Jan 12. PMID:14718529 doi:http://dx.doi.org/10.1074/jbc.M313580200
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