1fc4: Difference between revisions

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-[[Image:1fc4.gif|left|200px]]<br /><applet load="1fc4" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1fc4, resolution 2.0&Aring;" />
-'''2-AMINO-3-KETOBUTYRATE COA LIGASE'''<br />
-==Overview==
+==2-AMINO-3-KETOBUTYRATE COA LIGASE==
--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.
+<StructureSection load='1fc4' size='340' side='right'caption='[[1fc4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<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>
-FC4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with AKB as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycine_C-acetyltransferase Glycine C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.29 2.3.1.29] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FC4 OCA].
+</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='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>
-==Reference==
+<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>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11318637 11318637]
+</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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/1fc4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Glycine C-acetyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Cygler M]]
-[[Category: BSGI, Montreal-Kingston.Bacterial.Structural.Genomics.Initiative.]]
+[[Category: Larocque R]]
-[[Category: Cygler, M.]]
+[[Category: Li Y]]
-[[Category: Larocque, R.]]
+[[Category: Matte A]]
-[[Category: Li, Y.]]
+[[Category: Sauve V]]
-[[Category: Matte, A.]]
+[[Category: Schmidt A]]
-[[Category: Sauve, V.]]
+[[Category: Schrag JD]]
-[[Category: Schmidt, A.]]
+[[Category: Sivaraman J]]
-[[Category: Schrag, J.D.]]
+[[Category: Smith C]]
-[[Category: Sivaraman, J.]]
-[[Category: Smith, C.]]
-[[Category: AKB]]
-[[Category: 2-amino-3-ketobutyrate coa ligase]]
-[[Category: bsgi]]
-[[Category: coenzyme a]]
-[[Category: montreal-kingston bacterial structural genomics initiative]]
-[[Category: pyridoxal phosphate]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:48:37 2007''