1eil: Difference between revisions

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New page: left|200px<br /> <applet load="1eil" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eil, resolution 2.Å" /> '''2,3-DIHYDROXYBIPHENYL...
 
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[[Image:1eil.gif|left|200px]]<br />
<applet load="1eil" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1eil, resolution 2.&Aring;" />
'''2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE'''<br />


==Overview==
==2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE==
BphC derived from Pseudomonas sp. strain KKS102, an extradiol type, catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an, important role in the degradation of biphenyl/PCB (Poly Chlorinated, Biphenyls) in the microbe. Although we had earlier solved the crystal, structure of KKS102 BphC, it was the inactive form with Fe(III) in the, active site. In order to determine the active form structure, BphC was, re-activated by anaerobic incubation with Fe(II) and ascorbate, and, crystallized anaerobically. The crystal structures of activated BphC and, its substrate complex (E x S complex) were determined at 2.0 A resolution, under cryogenic condition. In addition, crystal structures of unactivated, BphC in substrate free and complex forms were also re-determined., Comparison of activated and unactivated E x S complexes reveals that the, orientation of the bound substrate in the active site is significantly, different between the two. The structural comparison of the substrate free, and complex forms of activated BphC show certain small conformational, shifts around the active site upon substrate binding. As a result of the, conformational shifts, His194, which has been suggested as the catalytic, base, takes part in a weak hydrogen bond with hydroxyl group of the, substrate.
<StructureSection load='1eil' size='340' side='right'caption='[[1eil]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1eil]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. The January 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Topoisomerases''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_1 10.2210/rcsb_pdb/mom_2006_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIL 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]] 2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1eil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eil OCA], [https://pdbe.org/1eil PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eil RCSB], [https://www.ebi.ac.uk/pdbsum/1eil PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eil 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/ei/1eil_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=1eil ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1EIL 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 SO4 and FE as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 1EIL with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb73_1.html Topoisomerases]]. 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=1EIL OCA].
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase., Uragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y, J Inorg Biochem. 2001 Feb;83(4):269-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11293547 11293547]
[[Category: Large Structures]]
[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
[[Category: Pseudomonas sp. KKS102]]
[[Category: Pseudomonas sp.]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Single protein]]
[[Category: Topoisomerases]]
[[Category: Topoisomerases]]
[[Category: Senda, T.]]
[[Category: Senda T]]
[[Category: FE]]
[[Category: SO4]]
[[Category: four repetitions of beta-alpha-beta-beta-beta motifs]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 08:59:29 2007''

Latest revision as of 10:03, 7 February 2024

2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE

Structural highlights

1eil is a 1 chain structure with sequence from Pseudomonas sp. KKS102. The January 2006 RCSB PDB Molecule of the Month feature on Topoisomerases by David S. Goodsell is 10.2210/rcsb_pdb/mom_2006_1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
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

1eil, resolution 2.00Å

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