PDBsum entry 3d03

Hydrolase

PDB id: 3d03

Contents

Protein chains

(+ 0 more) 274 a.a. *

Metals

_CO ×12

Waters ×1034

* Residue conservation analysis

PDB id:

3d03

Name:

Hydrolase

Title:

1.9a structure of glycerophoshphodiesterase (gpdq) from enterobacter aerogenes

Structure:

Phosphohydrolase. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Enterobacter aerogenes. Aerobacter aerogenes. Organism_taxid: 548. Gene: gpdq. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.186 R-free: 0.223

Authors:

K.S.Hadler,E.Tanifum,S.H.-C.Yip,N.Miti,L.W.Guddat,C.J.Jackson, L.R.Gahan,P.D.Carr,K.Nguyen,D.L.Ollis,A.C.Hengge,J.A.Larrabee, G.Schenk

Key ref:

K.S.Hadler et al. (2008). Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes. J Am Chem Soc, 130, 14129-14138. PubMed id: 18831553

Date:

30-Apr-08 Release date: 14-Oct-08

Protein chains

Q6XBH1  (GPDQ_KLEAE) -  Glycerophosphodiester phosphodiesterase GpdQ from Klebsiella aerogenes

Seq: 274 a.a.

Struc: 274 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.4.46 - glycerophosphodiester phosphodiesterase.
• Reaction: a sn-glycero-3-phosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate + H⁺

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

Added reference

J Am Chem Soc 130:14129-14138 (2008)

PubMed id: 18831553

Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes.

K.S.Hadler, E.A.Tanifum, S.H.Yip, N.Mitić, L.W.Guddat, C.J.Jackson, L.R.Gahan, K.Nguyen, P.D.Carr, D.L.Ollis, A.C.Hengge, J.A.Larrabee, G.Schenk.

ABSTRACT

The glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous binuclear metallohydrolase that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. GpdQ has attracted recent attention as a promising enzymatic bioremediator. Here, we have investigated the catalytic mechanism of this versatile enzyme using a range of techniques. An improved crystal structure (1.9 A resolution) illustrates the presence of (i) an extended hydrogen bond network in the active site, and (ii) two possible nucleophiles, i.e., water/hydroxide ligands, coordinated to one or both metal ions. While it is at present not possible to unambiguously distinguish between these two possibilities, a reaction mechanism is proposed whereby the terminally bound H2O/OH(-) acts as the nucleophile, activated via hydrogen bonding by the bridging water molecule. Furthermore, the presence of substrate promotes the formation of a catalytically competent binuclear center by significantly enhancing the binding affinity of one of the metal ions in the active site. Asn80 appears to display coordination flexibility that may modulate enzyme activity. Kinetic data suggest that the rate-limiting step occurs after hydrolysis, i.e., the release of the phosphate moiety and the concomitant dissociation of one of the metal ions and/or associated conformational changes. Thus, it is proposed that GpdQ employs an intricate regulatory mechanism for catalysis, where coordination flexibility in one of the two metal binding sites is essential for optimal activity.