2pcd
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION
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OverviewOverview
Protocatechuate 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.
About this StructureAbout this Structure
2PCD is a Protein complex structure of sequences from Pseudomonas putida with FE as ligand. This structure superseeds the now removed PDB entry 1PCD. Active as Protocatechuate 3,4-dioxygenase, with EC number 1.13.11.3 Full crystallographic information is available from OCA.
ReferenceReference
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
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