4co9: Difference between revisions

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 ==Crystal structure of kynurenine formamidase from Bacillus anthracis==
-<StructureSection load='4co9' size='340' side='right'  caption='[[4co9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='4co9' size='340' side='right'caption='[[4co9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4co9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_ames) Bacillus anthracis (strain ames)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CO9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CO9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4co9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Ames Bacillus anthracis str. Ames]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CO9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CO9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GXT:ETHANEDIAL'>GXT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4cob|4cob]], [[4cog|4cog]], [[4cz1|4cz1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=GXT:ETHANEDIAL'>GXT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arylformamidase Arylformamidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.9 3.5.1.9] </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=4co9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4co9 OCA], [https://pdbe.org/4co9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4co9 RCSB], [https://www.ebi.ac.uk/pdbsum/4co9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4co9 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4co9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4co9 OCA], [http://pdbe.org/4co9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4co9 RCSB], [http://www.ebi.ac.uk/pdbsum/4co9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4co9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KYNB_BACAN KYNB_BACAN]] Catalyzes the hydrolysis of N-formyl-L-kynurenine to L-kynurenine, the second step in the kynurenine pathway of tryptophan degradation (By similarity).
+[https://www.uniprot.org/uniprot/KYNB_BACAN KYNB_BACAN] Catalyzes the hydrolysis of N-formyl-L-kynurenine to L-kynurenine, the second step in the kynurenine pathway of tryptophan degradation (By similarity).
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalyzed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. Here, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment and unlike most Zn2+-dependent enzymes there is little scope to increase coordination number during catalysis. We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism.
-Structures of bacterial kynurenine formamidase reveal a crowded binuclear-zinc catalytic site primed to generate a potent nucleophile.,Diaz Saez L, Srikannathasan V, Zoltner M, Hunter WN Biochem J. 2014 Jun 19. PMID:24942958<ref>PMID:24942958</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4co9" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Arylformamidase]]
+[[Category: Bacillus anthracis str. Ames]]
-[[Category: Diaz-Saez, L]]
+[[Category: Large Structures]]
-[[Category: Hunter, W N]]
+[[Category: Diaz-Saez L]]
-[[Category: Srikannathasan, V]]
+[[Category: Hunter WN]]
-[[Category: Zoltner, M]]
+[[Category: Srikannathasan V]]
-[[Category: Aerobic tryptophan degradation via anthranilate]]
+[[Category: Zoltner M]]
-[[Category: Hydrolase]]