3rnb: Difference between revisions

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<StructureSection load='3rnb' size='340' side='right'caption='[[3rnb]], [[Resolution|resolution]] 2.64&Aring;' scene=''>
<StructureSection load='3rnb' size='340' side='right'caption='[[3rnb]], [[Resolution|resolution]] 2.64&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rnb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._ox1 Pseudomonas sp. ox1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RNB FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rnb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._OX1 Pseudomonas sp. OX1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RNB FirstGlance]. <br>
</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=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.64&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rn9|3rn9]], [[3rna|3rna]], [[3rnc|3rnc]], [[3rne|3rne]], [[3rnf|3rnf]], [[3rng|3rng]]</div></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=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">touA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1]), touB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320855 Pseudomonas sp. OX1])</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=3rnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rnb OCA], [https://pdbe.org/3rnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rnb RCSB], [https://www.ebi.ac.uk/pdbsum/3rnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rnb ProSAT]</span></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=3rnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rnb OCA], [https://pdbe.org/3rnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rnb RCSB], [https://www.ebi.ac.uk/pdbsum/3rnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rnb ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q6IV66_9PSED Q6IV66_9PSED]
For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/o-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the alpha-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O(2) migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O(2). This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/o-xylene monooxygenase hydroxylase are not artifacts of protein packing/folding, but rather programmed routes for dioxygen migration through the protein matrix. Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O(2) consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.
 
Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.,Song WJ, Gucinski G, Sazinsky MH, Lippard SJ Proc Natl Acad Sci U S A. 2011 Aug 22. PMID:21859951<ref>PMID:21859951</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3rnb" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pseudomonas sp. ox1]]
[[Category: Pseudomonas sp. OX1]]
[[Category: Gucinski, G]]
[[Category: Gucinski G]]
[[Category: Lippard, S J]]
[[Category: Lippard SJ]]
[[Category: Sazinsky, M H]]
[[Category: Sazinsky MH]]
[[Category: Song, W J]]
[[Category: Song WJ]]
[[Category: Diiron]]
[[Category: Four-helix bundle]]
[[Category: Hydroxylase]]
[[Category: Oxidoreductase]]
[[Category: Oxygen pathway]]
[[Category: Toluene]]

Latest revision as of 15:30, 14 March 2024

Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/F176W Double MutantStructure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/F176W Double Mutant

Structural highlights

3rnb is a 3 chain structure with sequence from Pseudomonas sp. OX1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.64Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6IV66_9PSED

See Also

3rnb, resolution 2.64Å

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