2pcd: Difference between revisions
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==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION== | ==STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION== | ||
<StructureSection load='2pcd' size='340' side='right' caption='[[2pcd]], [[Resolution|resolution]] 2.15Å' scene=''> | <StructureSection load='2pcd' size='340' side='right'caption='[[2pcd]], [[Resolution|resolution]] 2.15Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2pcd]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pcd 1pcd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PCD FirstGlance]. <br> | <table><tr><td colspan='2'>[[2pcd]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pcd 1pcd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PCD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PCD FirstGlance]. <br> | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/2pcd_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/2pcd_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2pcd" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2pcd" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Bacillus fluorescens putidus flugge 1886]] | [[Category: Bacillus fluorescens putidus flugge 1886]] | ||
[[Category: Large Structures]] | |||
[[Category: Protocatechuate 3,4-dioxygenase]] | [[Category: Protocatechuate 3,4-dioxygenase]] | ||
[[Category: Lipscomb, J D]] | [[Category: Lipscomb, J D]] | ||
Revision as of 18:31, 11 December 2019
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTIONSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION
Structural highlights
Function[PCXA_PSEPU] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. [PCXB_PSEPU] Plays an essential role in the utilization of numerous aromatic and hydroaromatic compounds via the beta-ketoadipate pathway. 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 PubMedProtocatechuate 3,4-dioxygenase catalyzes the aromatic ring cleavage of 3,4-dihydroxybenzoate by incorporating both atoms of molecular oxygen to yield beta-carboxy-cis,cis-muconate. The structure of this metalloenzyme from Pseudomonas aeruginosa (now reclassified as P. putida) has been refined to an R-factor of 0.172 to 2.15 A resolution. The structure is a highly symmetric (alpha beta Fe3+)12 aggregate with a root-mean-square (r.m.s.) difference of 0.18 A among symmetry-related atoms. The tertiary structure of the two polypeptides (alpha and beta) are highly homologous (r.m.s. difference of 1.05 A over 127 C alpha atoms), suggesting that the ancestral enzyme was originally a homodimer with two active sites. Indeed, a non-functional, vestigial active site retains many of the properties of the functional active site but does not bind iron. The coordination geometry of the non-heme iron catalytic cofactor can best be described as trigonal bipyramidal with Tyr447 (147 beta) and His462 (162 beta) serving as axial ligands, and Tyr408 (108 beta), His460 (160 beta) and Wat837 serving as equitorial ligands. The active site environment has a number of basic residues that may promote binding of the acidic substrate. Within the putative active site cavity which is located between alpha and beta chains, five approximately coplanar solvent molecules suggest a position for the planar substrate Trp449 (149 beta), Ile491 (191 beta), defined by Gly14 (14 alpha) and Pro15 (15 alpha). In this position the guanidino group of Arg457 (157 beta) would be buried by the substrate, suggesting a functional role in catalysis. Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution.,Ohlendorf DH, Orville AM, Lipscomb JD J Mol Biol. 1994 Dec 16;244(5):586-608. PMID:7990141[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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