1fc4: Difference between revisions

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 <StructureSection load='1fc4' size='340' side='right'caption='[[1fc4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1fc4]] is a 2 chain structure with sequence from [https://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=1FC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FC4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1fc4]] is a 2 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=1FC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FC4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKB:2-AMINO-3-KETOBUTYRIC+ACID'>AKB</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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&#8491;</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=AKB:2-AMINO-3-KETOBUTYRIC+ACID'>AKB</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycine_C-acetyltransferase Glycine C-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.29 2.3.1.29] </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=1fc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fc4 OCA], [https://pdbe.org/1fc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fc4 RCSB], [https://www.ebi.ac.uk/pdbsum/1fc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fc4 ProSAT], [https://www.topsan.org/Proteins/BSGI/1fc4 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/KBL_ECOLI KBL_ECOLI]] Catalyzes the cleavage of 2-amino-3-ketobutyrate to glycine and acetyl-CoA.<ref>PMID:2104756</ref>
+[https://www.uniprot.org/uniprot/KBL_ECOLI KBL_ECOLI] Catalyzes the cleavage of 2-amino-3-ketobutyrate to glycine and acetyl-CoA.<ref>PMID:2104756</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1fc4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
--Amino-3-ketobutyrate CoA ligase (KBL, EC 2.3.1.29) is a pyridoxal phosphate (PLP) dependent enzyme, which catalyzes the second reaction step on the main metabolic degradation pathway for threonine. It acts in concert with threonine dehydrogenase and converts 2-amino-3-ketobutyrate, the product of threonine dehydrogenation by the latter enzyme, with the participation of cofactor CoA, to glycine and acetyl-CoA. The enzyme has been well conserved during evolution, with 54% amino acid sequence identity between the Escherichia coli and human enzymes. We present the three-dimensional structure of E. coli KBL determined at 2.0 A resolution. KBL belongs to the alpha family of PLP-dependent enzymes, for which the prototypic member is aspartate aminotransferase. Its closest structural homologue is E. coli 8-amino-7-oxononanoate synthase. Like many other members of the alpha family, the functional form of KBL is a dimer, and one such dimer is found in the asymmetric unit in the crystal. There are two active sites per dimer, located at the dimer interface. Both monomers contribute side chains to each active/substrate binding site. Electron density maps indicated the presence in the crystal of the Schiff base intermediate of 2-amino-3-ketobutyrate and PLP, an external aldimine, which remained bound to KBL throughout the protein purification procedure. The observed interactions between the aldimine and the side chains in the substrate binding site explain the specificity for the substrate and provide the basis for a detailed proposal of the reaction mechanism of KBL. A putative binding site of the CoA cofactor was assigned, and implications for the cooperation with threonine dehydrogenase were considered.
-Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.,Schmidt A, Sivaraman J, Li Y, Larocque R, Barbosa JA, Smith C, Matte A, Schrag JD, Cygler M Biochemistry. 2001 May 1;40(17):5151-60. PMID:11318637<ref>PMID:11318637</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1fc4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Glycine C-acetyltransferase]]
 [[Category: Large Structures]]
-[[Category: Structural genomic]]
+[[Category: Cygler M]]
-[[Category: Cygler, M]]
+[[Category: Larocque R]]
-[[Category: Larocque, R]]
+[[Category: Li Y]]
-[[Category: Li, Y]]
+[[Category: Matte A]]
-[[Category: Matte, A]]
+[[Category: Sauve V]]
-[[Category: Sauve, V]]
+[[Category: Schmidt A]]
-[[Category: Schmidt, A]]
+[[Category: Schrag JD]]
-[[Category: Schrag, J D]]
+[[Category: Sivaraman J]]
-[[Category: Sivaraman, J]]
+[[Category: Smith C]]
-[[Category: Smith, C]]
-[[Category: 2-amino-3-ketobutyrate coa ligase]]
-[[Category: Bsgi]]
-[[Category: Coenzyme some]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transferase]]