1kw3: Difference between revisions

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New page: left|200px<br /><applet load="1kw3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kw3, resolution 1.450Å" /> '''Crystal structure o...
 
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[[Image:1kw3.jpg|left|200px]]<br /><applet load="1kw3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kw3, resolution 1.450&Aring;" />
'''Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution'''<br />


==Overview==
==Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution==
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.
<StructureSection load='1kw3' size='340' side='right'caption='[[1kw3]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kw3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KW3 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]] 1.45&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kw3 OCA], [https://pdbe.org/1kw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kw3 RCSB], [https://www.ebi.ac.uk/pdbsum/1kw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kw3 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/1kw3_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=1kw3 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KW3 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 FE2 and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KW3 OCA].
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12206778 12206778]
[[Category: Large Structures]]
[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
[[Category: Pseudomonas sp. KKS102]]
[[Category: Pseudomonas sp.]]
[[Category: Fukuda M]]
[[Category: Single protein]]
[[Category: Masai E]]
[[Category: Fukuda, M.]]
[[Category: Nishizaki T]]
[[Category: Masai, E.]]
[[Category: Nonaka T]]
[[Category: Nishizaki, T.]]
[[Category: Sato N]]
[[Category: Nonaka, T.]]
[[Category: Sazaki G]]
[[Category: Sato, N.]]
[[Category: Senda T]]
[[Category: Sazaki, G.]]
[[Category: Sugimoto K]]
[[Category: Senda, T.]]
[[Category: Takahashi Y]]
[[Category: Sugimoto, K.]]
[[Category: Uragami Y]]
[[Category: Takahashi, Y.]]
[[Category: Uragami, Y.]]
[[Category: FE2]]
[[Category: MPD]]
[[Category: four time repetitions of the beta-alpha-beta-beta-beta motif]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:57:10 2007''

Latest revision as of 16:26, 13 March 2024

Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolutionCrystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution

Structural highlights

1kw3 is a 1 chain structure with sequence from Pseudomonas sp. KKS102. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.45Å
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

1kw3, resolution 1.45Å

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