1bdb

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[[Image:1bdb.gif|left|200px]]<br />
 
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<applet load="1bdb" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bdb, resolution 2.0&Aring;" />
 
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'''CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400'''<br />
 
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==Overview==
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==CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400==
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cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the, aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal, structure of the NAD+-enzyme complex was determined by molecular, replacement and refined to an R-value of 17.9% at 2.0 A. As a member of, the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall, protein fold and positioning of the catalytic triad in BphB are very, similar to those observed in other SDR enzymes, although small differences, occur in the cofactor binding site. Modeling studies indicate that the, substrate is bound in a deep hydrophobic cleft close to the nicotinamide, moiety of the NAD+ cofactor. These studies further suggest that Asn143 is, a key determinant of substrate specificity. A two-step reaction mechanism, is proposed for cis-dihydrodiol dehydrogenases.
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<StructureSection load='1bdb' size='340' side='right'caption='[[1bdb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BDB 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]] 2&#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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bdb OCA], [https://pdbe.org/1bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bdb RCSB], [https://www.ebi.ac.uk/pdbsum/1bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bdb ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BPHB_PARXL BPHB_PARXL]
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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/bd/1bdb_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=1bdb 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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cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A. As a member of the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two-step reaction mechanism is proposed for cis-dihydrodiol dehydrogenases.
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==About this Structure==
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Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.,Hulsmeyer M, Hecht HJ, Niefind K, Hofer B, Eltis LD, Timmis KN, Schomburg D Protein Sci. 1998 Jun;7(6):1286-93. PMID:9655331<ref>PMID:9655331</ref>
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1BDB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Site: CAT. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BDB OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution., Hulsmeyer M, Hecht HJ, Niefind K, Hofer B, Eltis LD, Timmis KN, Schomburg D, Protein Sci. 1998 Jun;7(6):1286-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9655331 9655331]
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</div>
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[[Category: Pseudomonas sp.]]
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<div class="pdbe-citations 1bdb" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Hecht, H.J.]]
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[[Category: Hofer, B.]]
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[[Category: Huelsmeyer, M.]]
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[[Category: Niefind, K.]]
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[[Category: Schomburg, D.]]
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[[Category: Timmis, K.N.]]
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[[Category: NAD]]
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[[Category: nad-dependent oxidoreductase]]
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[[Category: pcb degradation]]
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[[Category: short-chain alcohol dehydrogenase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 15:53:53 2007''
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==See Also==
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*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Pseudomonas sp]]
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[[Category: Hecht H-J]]
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[[Category: Hofer B]]
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[[Category: Huelsmeyer M]]
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[[Category: Niefind K]]
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[[Category: Schomburg D]]
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[[Category: Timmis KN]]

Current revision

CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400

PDB ID 1bdb

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