1ukb

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[[Image:1ukb.png|left|200px]]
 
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{{STRUCTURE_1ukb| PDB=1ukb | SCENE= }}
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==Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with benzoate==
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<StructureSection load='1ukb' size='340' side='right'caption='[[1ukb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ukb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKB FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ukb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ukb OCA], [https://pdbe.org/1ukb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ukb RCSB], [https://www.ebi.ac.uk/pdbsum/1ukb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ukb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/P96965_PSEFL P96965_PSEFL]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uk/1ukb_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1ukb ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Meta-cleavage product hydrolase (MCP-hydrolase) is one of the key enzymes in the microbial degradation of aromatic compounds. MCP-hydrolase produces 2-hydroxypenta-2,4-dienoate and various organic acids, according to the C6 substituent of the substrate. Comprehensive analysis of the substrate specificity of the MCP-hydrolase from Pseudomonas fluorescens IP01 (CumD) was carried out by determining the kinetic parameters for nine substrates and crystal structures complexed with eight cleavage products. CumD preferred substrates with long non-branched C6 substituents, but did not effectively hydrolyze a substrate with a phenyl group. Superimposition of the complex structures indicated that benzoate was bound in a significantly different direction than other aliphatic cleavage products. The directions of the bound organic acids appeared to be related with the k(cat) values of the corresponding substrates. The Ile139 and Trp143 residues on helix alpha4 appeared to cause steric hindrance with the aromatic ring of the substrate, which hampers base-catalyzed attack by water.
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===Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with benzoate===
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A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products.,Fushinobu S, Jun SY, Hidaka M, Nojiri H, Yamane H, Shoun H, Omori T, Wakagi T Biosci Biotechnol Biochem. 2005 Mar;69(3):491-8. PMID:15784976<ref>PMID:15784976</ref>
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{{ABSTRACT_PUBMED_15784976}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 1ukb" style="background-color:#fffaf0;"></div>
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[[1ukb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKB OCA].
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== References ==
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<references/>
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==Reference==
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__TOC__
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<ref group="xtra">PMID:015784976</ref><references group="xtra"/>
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</StructureSection>
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[[Category: 2-hydroxymuconate-semialdehyde hydrolase]]
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[[Category: Large Structures]]
[[Category: Pseudomonas fluorescens]]
[[Category: Pseudomonas fluorescens]]
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[[Category: Fushinobu, S.]]
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[[Category: Fushinobu S]]
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[[Category: Hidaka, M.]]
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[[Category: Hidaka M]]
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[[Category: Jun, S Y.]]
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[[Category: Jun S-Y]]
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[[Category: Nojiri, H.]]
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[[Category: Nojiri H]]
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[[Category: Omori, T.]]
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[[Category: Omori T]]
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[[Category: Shoun, H.]]
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[[Category: Shoun H]]
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[[Category: Wakagi, T.]]
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[[Category: Wakagi T]]
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[[Category: Yamane, H.]]
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[[Category: Yamane H]]
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[[Category: Alpha/beta-hydrolase]]
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[[Category: Aromatic compound]]
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[[Category: Beta-ketolase]]
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[[Category: Cumene]]
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[[Category: Cumene degradation]]
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[[Category: Hydrolase]]
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[[Category: Isopropylbenzene]]
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[[Category: Meta-cleavage compound hydrolase]]
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[[Category: Pcb]]
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[[Category: Polychlorinated biphenyl degradation]]
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[[Category: Pseudomonas fluorescens ip01]]
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[[Category: Substrate specificity]]
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Current revision

Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with benzoate

PDB ID 1ukb

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