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| | <StructureSection load='3gzx' size='340' side='right'caption='[[3gzx]], [[Resolution|resolution]] 1.58Å' scene=''> | | <StructureSection load='3gzx' size='340' side='right'caption='[[3gzx]], [[Resolution|resolution]] 1.58Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3gzx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11996 Atcc 11996]. 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> | + | <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='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> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gzy|3gzy]], [[3gzz|3gzz]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285 ATCC 11996]), bphE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285 ATCC 11996])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Biphenyl_2,3-dioxygenase Biphenyl 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.18 1.14.12.18] </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=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> | | <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> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/BPHE_COMTE BPHE_COMTE]] The beta subunit may be responsible for the substrate specificity of the enzyme.
| + | [https://www.uniprot.org/uniprot/BPHA_COMTE BPHA_COMTE] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 11996]] | + | [[Category: Comamonas testosteroni]] |
| - | [[Category: Biphenyl 2,3-dioxygenase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bolin, J T]] | + | [[Category: Bolin JT]] |
| - | [[Category: Colbert, C L]] | + | [[Category: Colbert CL]] |
| - | [[Category: Kumar, P]] | + | [[Category: Kumar P]] |
| - | [[Category: Aromatic hydrocarbons catabolism]]
| + | |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Iron-sulfur]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Non-heme iron]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rieskie]]
| + | |
| Structural highlights
3gzx is a 2 chain structure with sequence from Comamonas testosteroni. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.58Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
BPHA_COMTE
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Colbert CL, Agar NY, Kumar P, Chakko MN, Sinha SC, Powlowski JB, Eltis LD, Bolin JT. Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes. PLoS One. 2013;8(1):e52550. doi: 10.1371/journal.pone.0052550. Epub 2013 Jan 3. PMID:23308114 doi:http://dx.doi.org/10.1371/journal.pone.0052550
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