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[[Image:1kw9.jpg|left|200px]]


{{Structure
==Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution==
|PDB= 1kw9 |SIZE=350|CAPTION= <scene name='initialview01'>1kw9</scene>, resolution 1.95&Aring;
<StructureSection load='1kw9' size='340' side='right'caption='[[1kw9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene> and <scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>
<table><tr><td colspan='2'>[[1kw9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1eim 1eim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KW9 FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BPY:BIPHENYL-2,3-DIOL'>BPY</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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=1kw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kw9 OCA], [https://pdbe.org/1kw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kw9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BPHC_PSES1 BPHC_PSES1]
== 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/kw/1kw9_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=1kw9 ConSurf].
<div style="clear:both"></div>


'''Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution'''
==See Also==
 
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
BphC derived from Pseudomonas sp. strain KKS102 is an extradiol-cleaving catecholic dioxygenase. This enzyme contains a non-heme iron atom and plays an important role in degrading biphenyl/polychlorinated biphenyls (PCBs) in the microbe. To elucidate detailed structures of BphC reaction intermediates, crystal structures of the substrate-free form, the BphC-substrate complex, and the BphC-substrate-NO (nitric oxide) complex were determined. These crystal structures revealed (1) the binding site of the O(2) molecule in the coordination sphere and (2) conformational changes of His194 during the catalytic reaction. On the basis of these findings, we propose a catalytic mechanism for the extradiol-cleaving catecholic dioxygenase in which His194 seems to play three distinct roles. At the early stage of the catalytic reaction, His194 appears to act as a catalytic base, which likely deprotonates the hydroxyl group of the substrate. At the next stage, the protonated His194 seems to stabilize a negative charge on the O2 molecule located in the hydrophobic O2-binding cavity. Finally, protonated His194 seems to function as a proton donor, whose existence has been proposed.
[[Category: Large Structures]]
 
[[Category: Pseudomonas sp. KKS102]]
==About this Structure==
[[Category: Fukuda M]]
1KW9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. This structure supersedes the now removed PDB entry 1EIM. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KW9 OCA].
[[Category: Masai E]]
 
[[Category: Nishizaki T]]
==Reference==
[[Category: Nonaka T]]
Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase., Sato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T, J Mol Biol. 2002 Aug 23;321(4):621-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12206778 12206778]
[[Category: Sato N]]
[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
[[Category: Sazaki G]]
[[Category: Pseudomonas sp.]]
[[Category: Senda T]]
[[Category: Single protein]]
[[Category: Sugimoto K]]
[[Category: Fukuda, M.]]
[[Category: Takahashi Y]]
[[Category: Masai, E.]]
[[Category: Uragami Y]]
[[Category: Nishizaki, T.]]
[[Category: Nonaka, T.]]
[[Category: Sato, N.]]
[[Category: Sazaki, G.]]
[[Category: Senda, T.]]
[[Category: Sugimoto, K.]]
[[Category: Takahashi, Y.]]
[[Category: Uragami, Y.]]
[[Category: BPY]]
[[Category: FE2]]
[[Category: four time repetitions of the beta-alpha-beta-beta-beta motif]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:23:01 2008''

Latest revision as of 16:26, 13 March 2024

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolutionCrystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution

Structural highlights

1kw9 is a 1 chain structure with sequence from Pseudomonas sp. KKS102. This structure supersedes the now removed PDB entry 1eim. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BPHC_PSES1

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kw9, resolution 1.95Å

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