PDBsum entry 2dvt

Lyase

PDB id: 2dvt

Contents

Protein chains

325 a.a. *

Metals

_ZN ×4

Waters ×1223

* Residue conservation analysis

PDB id:

2dvt

Name:

Lyase

Title:

Crystal structure of 2,6-dihydroxybenzoate decarboxylase from rhizobium

Structure:

Thermophilic reversible gamma-resorcylate decarboxylase. Chain: a, b, c, d. Synonym: 2,6-dihydroxybenzoate decarboxylase. Ec: 4.1.1.-

Source:

Rhizobium sp.. Organism_taxid: 267998. Strain: mtp-10005

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.180 R-free: 0.200

Authors:

M.Goto

Key ref:

M.Goto et al. (2006). Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. J Biol Chem, 281, 34365-34373. PubMed id: 16963440 DOI: 10.1074/jbc.M607270200

Date:

01-Aug-06 Release date: 19-Sep-06

Protein chains

Q60GU1  (GRDC_RHIS5) -  Gamma-resorcylate decarboxylase from Rhizobium sp. (strain MTP-10005)

Seq: 327 a.a.

Struc: 325 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.103 - gamma-resorcylate decarboxylase.
• Reaction: 2,6-dihydroxybenzoate + H⁺ = resorcinol + CO2
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M607270200

J Biol Chem 281:34365-34373 (2006)

PubMed id: 16963440

Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005.

M.Goto, H.Hayashi, I.Miyahara, K.Hirotsu, M.Yoshida, T.Oikawa.

ABSTRACT

Reversible 2,6-dihydroxybenzoate decarboxylase from Rhizobium sp. strain MTP-10005 belongs to a nonoxidative decarboxylase family. We have determined the structures of the following three forms of the enzyme: the native form, the complex with the true substrate (2,6-dihydroxybenzoate), and the complex with 2,3-dihydroxybenzaldehyde at 1.7-, 1.9-, and 1.7-A resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of one (alphabeta)8 triose-phosphate isomerase-barrel domain with three functional linkers and one C-terminal tail. The native enzyme possesses one Zn2+ ion liganded by Glu8, His10, His164, Asp287, and a water molecule at the active site center, although the enzyme has been reported to require no cofactor for its catalysis. The substrate carboxylate takes the place of the water molecule and is coordinated to the Zn2+ ion. The 2-hydroxy group of the substrate is hydrogen-bonded to Asp287, which forms a triad together with His218 and Glu221 and is assumed to be the catalytic base. On the basis of the geometrical consideration, substrate specificity is uncovered, and the catalytic mechanism is proposed for the novel Zn2+-dependent decarboxylation.

Selected figure(s)

Figure 3.
FIGURE 3. Schematic diagram showing hydrogen bond and coordinate bond interactions. Putative hydrogen bond interactions are shown by dotted lines if the acceptor and donor are less than 3.5 Å apart. Coordinate bonds between Zn^2+ ion and the active site residues are shown by solid lines if Zn^2+ ion and the ligand are less than 2.2 Å apart. A, GRCD in the native form. B, GRCD·2,6-dihydroxybenzoate complex. C, GRCD·2,3-dihydroxybenzaldehyde complex.

Figure 4.
FIGURE 4. Proposed reaction mechanism for decarboxylation in 2,6-dihydroxybenzoate decarboxylase.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 34365-34373) copyright 2006.

Figures were selected by an automated process.