3gzx
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3gzx is ON HOLD until sometime in the future Authors: Kumar, P., Colbert, C.L., Bolin, J.T. Description: Crystal Structure of the Biphenyl Dioxygen...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356== | |
| + | <StructureSection load='3gzx' size='340' side='right'caption='[[3gzx]], [[Resolution|resolution]] 1.58Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3gzx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZX FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58Å</td></tr> | ||
| + | <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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></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=3gzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gzx OCA], [https://pdbe.org/3gzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gzx RCSB], [https://www.ebi.ac.uk/pdbsum/3gzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gzx ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/BPHA_COMTE BPHA_COMTE] | ||
| + | == 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/gz/3gzx_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=3gzx ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a heterohexameric (alphabeta)(3) Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356) with and without its substrate biphenyl 1.6-A resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nepsilon2, H239 Nepsilon2, D386 Odelta1 and Odelta2, and a single water molecule. Analysis of the active sites of BPDO(B356) and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments. | ||
| - | + | Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes.,Colbert CL, Agar NY, Kumar P, Chakko MN, Sinha SC, Powlowski JB, Eltis LD, Bolin JT PLoS One. 2013;8(1):e52550. doi: 10.1371/journal.pone.0052550. Epub 2013 Jan 3. PMID:23308114<ref>PMID:23308114</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 3gzx" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Comamonas testosteroni]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Bolin JT]] | ||
| + | [[Category: Colbert CL]] | ||
| + | [[Category: Kumar P]] | ||
Current revision
Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356
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