1ulj

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[[Image:1ulj.png|left|200px]]
 
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==Biphenyl dioxygenase (BphA1A2) in complex with the substrate==
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The line below this paragraph, containing "STRUCTURE_1ulj", creates the "Structure Box" on the page.
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<StructureSection load='1ulj' size='340' side='right'caption='[[1ulj]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ulj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_jostii_RHA1 Rhodococcus jostii RHA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ULJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ULJ FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.6&#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=BNL:BIPHENYL'>BNL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
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{{STRUCTURE_1ulj| PDB=1ulj | SCENE= }}
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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=1ulj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ulj OCA], [https://pdbe.org/1ulj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ulj RCSB], [https://www.ebi.ac.uk/pdbsum/1ulj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ulj ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BPHA1_RHOJR BPHA1_RHOJR] Part of the oxygenase component of the biphenyl dioxygenase system that catalyzes the stereospecific dihydroxylation of the aromatic ring of biphenyl, yielding a dihydrodiol compound. Is essential for biphenyl degradation and growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole source of carbon and energy. Can also use naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-2S] cluster of BphA3.<ref>PMID:17420585</ref> <ref>PMID:7793929</ref>
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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/ul/1ulj_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=1ulj 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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Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.
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===Biphenyl dioxygenase (BphA1A2) in complex with the substrate===
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Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.,Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T J Mol Biol. 2004 Sep 17;342(3):1041-52. PMID:15342255<ref>PMID:15342255</ref>
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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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<div class="pdbe-citations 1ulj" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15342255}}, adds the Publication Abstract to the page
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15342255 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15342255}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[1ulj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_jostii_rha1 Rhodococcus jostii rha1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ULJ OCA].
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[[Category: Rhodococcus jostii RHA1]]
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[[Category: Fukuda M]]
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==Reference==
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[[Category: Furusawa Y]]
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<ref group="xtra">PMID:15342255</ref><ref group="xtra">PMID:14529495</ref><references group="xtra"/>
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[[Category: Masai E]]
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[[Category: Biphenyl 2,3-dioxygenase]]
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[[Category: Nagarajan V]]
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[[Category: Rhodococcus jostii rha1]]
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[[Category: Senda T]]
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[[Category: Fukuda, M.]]
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[[Category: Tanokura M]]
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[[Category: Furusawa, Y.]]
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[[Category: Masai, E.]]
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[[Category: Nagarajan, V.]]
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[[Category: Senda, T.]]
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[[Category: Tanokura, M.]]
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[[Category: Alpha3 beta3 hetero hexamer]]
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[[Category: Oxidoreductase]]
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Current revision

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

PDB ID 1ulj

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