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| | <StructureSection load='2ahu' size='340' side='right'caption='[[2ahu]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='2ahu' size='340' side='right'caption='[[2ahu]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ahu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AHU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ahu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AHU FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ahv|2ahv]], [[2ahw|2ahw]]</div></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></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YdiF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=2ahu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ahu OCA], [https://pdbe.org/2ahu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ahu RCSB], [https://www.ebi.ac.uk/pdbsum/2ahu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ahu 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=2ahu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ahu OCA], [https://pdbe.org/2ahu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ahu RCSB], [https://www.ebi.ac.uk/pdbsum/2ahu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ahu ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/YDIF_ECO57 YDIF_ECO57]] CoA transferase having broad substrate specificity for short-chain acyl-CoA thioesters with the activity decreasing when the length of the carboxylic acid chain exceeds four carbons. Exhibits high activity with acetoacetyl-CoA, propionyl-CoA, crotonoyl-CoA or butyryl-CoA as donors, with acetate as an acceptor. When acetyl-CoA is used as the donor, propionate, acetoacetate, butyrate, isobutyrate, and 4-hydroxybutyrate can be utilized as acceptors but not isovalerate. May play a role in short-chain fatty acid metabolism in E.coli.<ref>PMID:16253988</ref>
| + | [https://www.uniprot.org/uniprot/YDIF_ECO57 YDIF_ECO57] CoA transferase having broad substrate specificity for short-chain acyl-CoA thioesters with the activity decreasing when the length of the carboxylic acid chain exceeds four carbons. Exhibits high activity with acetoacetyl-CoA, propionyl-CoA, crotonoyl-CoA or butyryl-CoA as donors, with acetate as an acceptor. When acetyl-CoA is used as the donor, propionate, acetoacetate, butyrate, isobutyrate, and 4-hydroxybutyrate can be utilized as acceptors but not isovalerate. May play a role in short-chain fatty acid metabolism in E.coli.<ref>PMID:16253988</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: Eco57]] | + | [[Category: Escherichia coli O157:H7]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ajamian, E]] | + | [[Category: Ajamian E]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Cygler M]] |
| - | [[Category: Cygler, M]] | + | [[Category: Fraser ME]] |
| - | [[Category: Fraser, M E]] | + | [[Category: Iannuzzi P]] |
| - | [[Category: Iannuzzi, P]] | + | [[Category: Kernaghan SD]] |
| - | [[Category: Kernaghan, S D]] | + | [[Category: Li Y]] |
| - | [[Category: Li, Y]] | + | [[Category: Matte A]] |
| - | [[Category: Matte, A]] | + | [[Category: Rangarajan ES]] |
| - | [[Category: Rangarajan, E S]] | + | |
| - | [[Category: Bsgi]]
| + | |
| - | [[Category: Coa transferase]]
| + | |
| - | [[Category: Glutamyl thioester]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Ydif]]
| + | |
| Structural highlights
Function
YDIF_ECO57 CoA transferase having broad substrate specificity for short-chain acyl-CoA thioesters with the activity decreasing when the length of the carboxylic acid chain exceeds four carbons. Exhibits high activity with acetoacetyl-CoA, propionyl-CoA, crotonoyl-CoA or butyryl-CoA as donors, with acetate as an acceptor. When acetyl-CoA is used as the donor, propionate, acetoacetate, butyrate, isobutyrate, and 4-hydroxybutyrate can be utilized as acceptors but not isovalerate. May play a role in short-chain fatty acid metabolism in E.coli.[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
Coenzyme A transferases are involved in a broad range of biochemical processes in both prokaryotes and eukaryotes, and exhibit a diverse range of substrate specificities. The YdiF protein from Escherichia coli O157:H7 is an acyl-CoA transferase of unknown physiological function, and belongs to a large sequence family of CoA transferases, present in bacteria to humans, which utilize oxoacids as acceptors. In vitro measurements showed that YdiF displays enzymatic activity with short-chain acyl-CoAs. The crystal structures of YdiF and its complex with CoA, the first co-crystal structure for any Family I CoA transferase, have been determined and refined at 1.9 and 2.0 A resolution, respectively. YdiF is organized into tetramers, with each monomer having an open alpha/beta structure characteristic of Family I CoA transferases. Co-crystallization of YdiF with a variety of CoA thioesters in the absence of acceptor carboxylic acid resulted in trapping a covalent gamma-glutamyl-CoA thioester intermediate. The CoA binds within a well defined pocket at the N- and C-terminal domain interface, but makes contact only with the C-terminal domain. The structure of the YdiF complex provides a basis for understanding the different catalytic steps in the reaction of Family I CoA transferases.
Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases.,Rangarajan ES, Li Y, Ajamian E, Iannuzzi P, Kernaghan SD, Fraser ME, Cygler M, Matte A J Biol Chem. 2005 Dec 30;280(52):42919-28. Epub 2005 Oct 27. PMID:16253988[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Rangarajan ES, Li Y, Ajamian E, Iannuzzi P, Kernaghan SD, Fraser ME, Cygler M, Matte A. Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases. J Biol Chem. 2005 Dec 30;280(52):42919-28. Epub 2005 Oct 27. PMID:16253988 doi:10.1074/jbc.M510522200
- ↑ Rangarajan ES, Li Y, Ajamian E, Iannuzzi P, Kernaghan SD, Fraser ME, Cygler M, Matte A. Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases. J Biol Chem. 2005 Dec 30;280(52):42919-28. Epub 2005 Oct 27. PMID:16253988 doi:10.1074/jbc.M510522200
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