PDBsum entry: 1f5s

Hydrolase

PDB id: 1f5s

Contents

Protein chains

210 a.a. *

Ligands

PO4 ×4

Metals

_MG ×2

Waters ×383

* Residue conservation analysis

PDB id:

1f5s

Name:

Hydrolase

Title:

Crystal structure of phosphoserine phosphatase from methanococcus jannaschii

Structure:

Phosphoserine phosphatase (psp). Chain: a, b. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Strain: mj1594. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.198 R-free: 0.235

Authors:

W.Wang,R.Kim,J.Jancarik,H.Yokota,S.H.Kim,Berkeley Structural Genomics Center (Bsgc)

Key ref:

W.Wang et al. (2001). Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution. Structure, 9, 65-71. PubMed id: 11342136 DOI: 10.1016/S0969-2126(00)00558-X

Date:

15-Jun-00 Release date: 20-Jun-01

Protein chains

Q58989  (SERB_METJA) -  Phosphoserine phosphatase

Seq: 211 a.a.

Struc: 210 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.3 - Phosphoserine phosphatase.
• Reaction: O-phospho-L(or D)-serine + H₂O = L(or D)-serine + phosphate

O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (5 terms)

Key reference

DOI no: 10.1016/S0969-2126(00)00558-X

Structure 9:65-71 (2001)

PubMed id: 11342136

Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution.

W.Wang, R.Kim, J.Jancarik, H.Yokota, S.H.Kim.

ABSTRACT

BACKGROUND: D-Serine is a co-agonist of the N-methyl-D-aspartate subtype of glutamate receptors, a major neurotransmitter receptor family in mammalian nervous systems. D-Serine is converted from L-serine, 90% of which is the product of the enzyme phosphoserine phosphatase (PSP). PSP from M. jannaschii (MJ) shares significant sequence homology with human PSP. PSPs and P-type ATPases are members of the haloacid dehalogenase (HAD)-like hydrolase family, and all members share three conserved sequence motifs. PSP and P-type ATPases utilize a common mechanism that involves Mg(2+)-dependent phosphorylation and autodephosphorylation at an aspartyl side chain in the active site. The strong resemblance in sequence and mechanism implies structural similarity among these enzymes. RESULTS: The PSP crystal structure resembles the NAD(P) binding Rossmann fold with a large insertion of a four-helix-bundle domain and a beta hairpin. Three known conserved sequence motifs are arranged next to each other in space and outline the active site. A phosphate and a magnesium ion are bound to the active site. The active site is within a closed environment between the core alpha/beta domain and the four-helix-bundle domain. CONCLUSIONS: The crystal structure of MJ PSP was determined at 1.8 A resolution. Critical residues were assigned based on the active site structure and ligand binding geometry. The PSP structure is in a closed conformation that may resemble the phosphoserine bound state or the state after autodephosphorylation. Compared to a P-type ATPase (Ca(2+)-ATPase) structure, which is in an open state, this PSP structure appears also to be a good model for the closed conformation of P-type ATPase.

Selected figure(s)

Figure 2.
Figure 2. Ribbon Diagram of PSP Structure and Hydrogen Bond Network of Its Active Site(a) Stereo view of the PSP structure presented in a ribbon diagram. The three conserved motifs are colored in red. The orange molecule depicts the phosphate in the active site. The green ball depicts the Mg2+ ion.(b) A schematic plot of the hydrogen bond network in the active site. All the H bonds that involve the ligands, and part of the H-bonds that do not involve the ligands, are shown as dotted lines. The unit for the distances is in Å. The Mg2+ achieves the hexavalent coordination through interactions with the phosphate, Asp-11, Asp-13, Asp-167, and water molecules W222 and W223. W222 and W223, in turn, interact with the surrounding residues including Asp-167, Glu-20, Asp-171, Asp-170, and the phosphate. Asp-11 adopts discrete sidechain conformations 1 and 2. Both conformations coordinate with the Mg2+. Conformer 1 also interacts with the phosphate while conformer 2 is remote form the phosphate but forms an H bond with the Thr-15 sidechain. The phosphate forms H bonds with residues from all three motifs. The H bond between O1 and Asp-11 suggests that either O1 or Asp-11 is protonated.

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 65-71) copyright 2001.

Figure was selected by the author.