PDBsum entry 1wzc

Hydrolase

PDB id: 1wzc

Contents

Protein chains

234 a.a. *

Ligands

PO4 ×2

Metals

_MG ×2

Waters ×102

* Residue conservation analysis

PDB id:

1wzc

Name:

Hydrolase

Title:

Crystal structure of pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase complexed with mg2+ and phosphate

Structure:

Mannosyl-3-phosphoglycerate phosphatase. Chain: a, b. Synonym: mpgp. Engineered: yes. Mutation: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: ph0926. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.219 R-free: 0.253

Authors:

T.Kawamura,N.Watanabe,I.Tanaka

Key ref:

T.Kawamura et al. (2008). Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr, 64, 1267-1276. PubMed id: 19018103 DOI: 10.1107/S0907444908033817

Date:

04-Mar-05 Release date: 28-Feb-06

Protein chains

O58690  (MPGP_PYRHO) -  Mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 243 a.a.

Struc: 234 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.3.70 - mannosyl-3-phosphoglycerate phosphatase.
• Reaction: 2-O-(alpha-D-mannosyl)-3-phosphoglycerate + H2O = (2R)-2-O-(alpha-D- mannosyl)-glycerate + phosphate

2-O-(alpha-D-mannosyl)-3-phosphoglycerate + H2O = (2R)-2-O-(alpha-D- mannosyl)-glycerate + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Cofactor: Mg(2+)

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

Key reference

DOI no: 10.1107/S0907444908033817

Acta Crystallogr D Biol Crystallogr 64:1267-1276 (2008)

PubMed id: 19018103

Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii.

T.Kawamura, N.Watanabe, I.Tanaka.

ABSTRACT

Mannosyl-3-phosphoglycerate phosphatase (MPGP) catalyzes the dephosphorylation of alpha-mannosyl-3-phosphoglycerate (MPG) to produce alpha-mannosylglycerate (MG). In the hyperthermophile Pyrococcus horikoshii, MPGP plays a role in a series of enzyme reactions that are involved in the MG-biosynthesis pathway, which is important for maintaining life under conditions of high salt concentration. Crystal structures of P. horikoshii MPGP (PhoMPGP) in the holo form and in the apo form lacking the magnesium ion were determined by the multiple-wavelength anomalous diffraction method using SeMet-substituted PhoMPGP. PhoMPGP consists of two domains: a core domain that is conserved in the haloacid dehalogenase superfamily and a cap domain that is specific to the C2B cap subclass of the superfamily. Apo-form crystals contain two PhoMPGP molecules: one in the open conformation and the other in the closed conformation. In holo-form crystals both of the two molecules are in the closed conformation with phosphate and magnesium ions. PhoMPGP has a specific hairpin loop that is bent towards the active site in the closed conformation of both the apo and holo forms. PhoMPGP has a cavity between the two domains which is considered to be the substrate-binding site as a phosphate ion is located in the cavity, mimicking the binding manner of the phosphate group of MPG. The cavity is sequestered in the closed conformation such that a conformational change is indispensable for the release of products. A salt bridge from the general acid/base Asp10 to Arg170 is observed in the holo-form PhoMPGP which is not present in the open form. The importance of the conformational change in the activity of PhoMPGP is discussed.

Selected figure(s)

Figure 3.
Figure 3 Monomer structures observed in PhoMPGP crystals. (a) Apo-form open conformation. (b) Apo-form closed conformation. (c) Holo-form closed conformation, with the phosphate and magnesium ions shown as a stick model and as a sphere, respectively.

Figure 7.
Figure 7 Molecular surfaces of (a) apo-form PhoMPGP open conformation, (b) apo-form PhoMPGP closed conformation and (c) holo-form PhoMPGP. The sequestered surface in (c) is indicated in dark grey in (a) and (b). (d) Ribbon model of holo-form PhoMPGP viewed from the same angle as in (c). In (d), the phosphate and magnesium ions are indicated by a stick model and as a sphere, respectively. The mesh indicates the cavity detected by the program VOIDOO (Kleywegt & Jones, 1994[Kleywegt, G. J. & Jones, T. A. (1994). Acta Cryst. D50, 178-185.]) with a probe 1.4 Å in radius. The cavity had an ovoid-like shape with one protrusion where the phosphate ion binds in the active site.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 1267-1276) copyright 2008.

Figures were selected by an automated process.