PDBsum entry 1eo2

Oxidoreductase

PDB id: 1eo2

Contents

Protein chains

202 a.a. *

238 a.a. *

Metals

_FE

Waters ×183

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Structure of acinetobacter strain ADP1 protocatechuate 3, 4-Dioxygenase at 2.2 a resolution: implications for the mechanism of an intradiol dioxygenase.
• Authors: M.W.Vetting, D.A.D'Argenio, L.N.Ornston, D.H.Ohlendorf.
• Ref.: Biochemistry, 2000, 39, 7943-7955. [DOI no: 10.1021/bi000151e]
• PubMed id: 10891075

Abstract

The crystal structures of protocatechuate 3,4-dioxygenase from the soil bacteria Acinetobacterstrain ADP1 (Ac 3,4-PCD) have been determined in space group I23 at pH 8.5 and 5.75. In addition, the structures of Ac 3,4-PCD complexed with its substrate 3, 4-dihydroxybenzoic acid (PCA), the inhibitor 4-nitrocatechol (4-NC), or cyanide (CN(-)) have been solved using native phases. The overall tertiary and quaternary structures of Ac 3,4-PCD are similar to those of the same enzyme from Pseudomonas putida[Ohlendorf et al. (1994) J. Mol. Biol. 244, 586-608]. At pH 8.5, the catalytic non-heme Fe(3+) is coordinated by two axial ligands, Tyr447(OH) (147beta) and His460(N)(epsilon)(2) (160beta), and three equatorial ligands, Tyr408(OH) (108beta), His462(N)(epsilon)(2) (162beta), and a hydroxide ion (d(Fe-OH) = 1.91 A) in a distorted bipyramidal geometry. At pH 5.75, difference maps suggest a sulfate binds to the Fe(3+) in an equatorial position and the hydroxide is shifted [d(Fe-OH) = 2.3 A] yielding octahedral geometry for the active site Fe(3+). This change in ligation geometry is concomitant with a shift in the optical absorbance spectrum of the enzyme from lambda(max) = 450 nm to lambda(max) = 520 nm. Binding of substrate or 4-NC to the Fe(3+) is bidentate with the axial ligand Tyr447(OH) (147beta) dissociating. The structure of the 4-NC complex supports the view that resonance delocalization of the positive character of the nitrogen prevents substrate activation. The cyanide complex confirms previous work that protocatechuate 3,4-dioxygenases have three coordination sites available for binding by exogenous substrates. A significant conformational change extending away from the active site is seen in all structures when compared to the native enzyme at pH 8.5. This conformational change is discussed in its relevance to enhancing catalysis in protocatechuate 3,4-dioxygenases.

Secondary reference #1

• Title: Crystallization and preliminary X-Ray analysis of protocatechuate 3,4-Dioxygenase from acinetobacter calcoaceticus.
• Authors: M.W.Vetting, C.A.Earhart, D.H.Ohlendorf.
• Ref.: J Mol Biol, 1994, 236, 372-373.
• PubMed id: 8107118

Secondary reference #2

• Title: Substitution, Insertion, Deletion, Suppression, And altered substrate specificity in functional protocatechuate 3,4-Dioxygenases.
• Authors: D.A.D'Argenio, M.W.Vetting, D.H.Ohlendorf, L.N.Ornston.
• Ref.: J Bacteriol, 1999, 181, 6478-6487.
• PubMed id: 10515940

Secondary reference #3

• Title: Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-Dioxygenase: endogenous fe3+ ligand displacement in response to substrate binding.
• Authors: A.M.Orville, J.D.Lipscomb, D.H.Ohlendorf.
• Ref.: Biochemistry, 1997, 36, 10052-10066. [DOI no: 10.1021/bi970469f]
• PubMed id: 9254600

Secondary reference #4

• Title: Structure of protocatechuate 3,4-Dioxygenase from pseudomonas aeruginosa at 2.15 a resolution.
• Authors: D.H.Ohlendorf, A.M.Orville, J.D.Lipscomb.
• Ref.: J Mol Biol, 1994, 244, 586-608.
• PubMed id: 7990141