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2rdb

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X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

Structural highlights

2rdb is a 3 chain structure with sequence from Pseudomonas stutzeri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O87798_STUST

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

At its carboxylate-bridged diiron active site, the hydroxylase component of toluene/o-xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. In an I100W variant of this enzyme, we characterized the formation and decay of two species formed by addition of dioxygen to the reduced, diiron(II) state by rapid-freeze quench (RFQ) EPR, Mossbauer, and ENDOR spectroscopy. The dependence of the formation and decay rates of this mixed-valent transient on pH and the presence of phenol, propylene, or acetylene was investigated by double-mixing stopped-flow optical spectroscopy. Modification of the alpha-subunit of the hydroxylase after reaction of the reduced protein with dioxygen-saturated buffer was investigated by tryptic digestion coupled mass spectrometry. From these investigations, we conclude that (i) a diiron(III,IV)-W* transient, kinetically linked to a preceding diiron(III) intermediate, arises from the one-electron oxidation of W100, (ii) the tryptophan radical is deprotonated, (iii) rapid exchange of either a terminal water or hydroxide ion with water occurs at the ferric ion in the diiron(III,IV) cluster, and (iv) the diiron(III,IV) core and W* decay to the diiron(III) product by a common mechanism. No transient radical was observed by stopped-flow optical spectroscopy for reactions of the reduced hydroxylase variants I100Y, L208F, and F205W with dioxygen. The absence of such species, and the deprotonated state of the tryptophanyl radical in the diiron(III,IV)-W* transient, allow for a conservative estimate of the reduction potential of the diiron(III) intermediate as lying between 1.1 and 1.3 V. We also describe the X-ray crystal structure of the I100W variant of ToMOH.

Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase.,Murray LJ, Garcia-Serres R, McCormick MS, Davydov R, Naik SG, Kim SH, Hoffman BM, Huynh BH, Lippard SJ Biochemistry. 2007 Dec 25;46(51):14795-809. Epub 2007 Nov 29. PMID:18044971^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Murray LJ, Garcia-Serres R, McCormick MS, Davydov R, Naik SG, Kim SH, Hoffman BM, Huynh BH, Lippard SJ. Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase. Biochemistry. 2007 Dec 25;46(51):14795-809. Epub 2007 Nov 29. PMID:18044971 doi:10.1021/bi7017128

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rdb"

@@ Line 1: / Line 1: @@
 ==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==
-<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2rdb' size='340' side='right'caption='[[2rdb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2inc|2inc]], [[2ind|2ind]], [[1t0q|1t0q]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [https://pdbe.org/2rdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [https://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://pdbe.org/2rdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O87798_STUST O87798_STUST]
 == 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/rd/2rdb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdb_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 2rdb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Achromobacter sewerinii bergey et al. 1923]]
+[[Category: Large Structures]]
-[[Category: Davydov, R]]
+[[Category: Pseudomonas stutzeri]]
-[[Category: Garcia-Serres, R]]
+[[Category: Davydov R]]
-[[Category: Hoffman, B M]]
+[[Category: Garcia-Serres R]]
-[[Category: Huynh, B H]]
+[[Category: Hoffman BM]]
-[[Category: Lippard, S J]]
+[[Category: Huynh BH]]
-[[Category: McCormick, M S]]
+[[Category: Lippard SJ]]
-[[Category: Murray, L J]]
+[[Category: McCormick MS]]
-[[Category: Naik, S]]
+[[Category: Murray LJ]]
-[[Category: 4-helix bundle]]
+[[Category: Naik S]]
-[[Category: Carboxylate bridge]]
-[[Category: Diiron]]
-[[Category: Metalloenzyme]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Tryptophan radical]]

2rdb

From Proteopedia

Current revision

X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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