PDBsum entry 1l7o

Hydrolase

PDB id: 1l7o

Contents

Protein chains

200 a.a. *

Ligands

ACY ×2

Metals

_ZN ×3

Waters ×140

* Residue conservation analysis

PDB id:

1l7o

Name:

Hydrolase

Title:

Crystal structure of phosphoserine phosphatase in apo form

Structure:

Phosphoserine phosphatase. Chain: a, b. Synonym: psp, o-phosphoserine phosphohydrolase, pspase. Engineered: yes. Mutation: yes

Source:

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

Resolution:

2.20Å R-factor: 0.224 R-free: 0.254

Authors:

W.Wang,H.S.Cho,R.Kim,J.Jancarik,H.Yokota,H.H.Nguyen,I.V.Grigoriev, D.E.Wemmer,S.H.Kim,Berkeley Structural Genomics Center (Bsgc)

Key ref:

W.Wang et al. (2002). Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. J Mol Biol, 319, 421-431. PubMed id: 12051918 DOI: 10.1016/S0022-2836(02)00324-8

Date:

16-Mar-02 Release date: 19-Jun-02

Protein chains

Q58989  (SERB_METJA) -  Phosphoserine phosphatase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 211 a.a.

Struc: 200 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.3.3 - phosphoserine phosphatase.
• Reaction:
  1. O-phospho-L-serine + H2O = L-serine + phosphate
  2. O-phospho-D-serine + H2O = D-serine + phosphate

O-phospho-L-serine + H2O = L-serine (Bound ligand (Het Group name = ACY) matches with 57.14% similarity) + phosphate

O-phospho-D-serine + H2O = D-serine (Bound ligand (Het Group name = ACY) matches with 57.14% similarity) + phosphate

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

reference

DOI no: 10.1016/S0022-2836(02)00324-8

J Mol Biol 319:421-431 (2002)

PubMed id: 12051918

Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states.

W.Wang, H.S.Cho, R.Kim, J.Jancarik, H.Yokota, H.H.Nguyen, I.V.Grigoriev, D.E.Wemmer, S.H.Kim.

ABSTRACT

Phosphoserine phosphatase (PSP) is a member of a large class of enzymes that catalyze phosphoester hydrolysis using a phosphoaspartate-enzyme intermediate. PSP is a likely regulator of the steady-state d-serine level in the brain, which is a critical co-agonist of the N-methyl-d-aspartate type of glutamate receptors. Here, we present high-resolution (1.5-1.9 A) structures of PSP from Methanococcus jannaschii, which define the open state prior to substrate binding, the complex with phosphoserine substrate bound (with a D to N mutation in the active site), and the complex with AlF3, a transition-state analog for the phospho-transfer steps in the reaction. These structures, together with those described for the BeF3- complex (mimicking the phospho-enzyme) and the enzyme with phosphate product in the active site, provide a detailed structural picture of the full reaction cycle. The structure of the apo state indicates partial unfolding of the enzyme to allow substrate binding, with refolding in the presence of substrate to provide specificity. Interdomain and active-site conformational changes are identified. The structure with the transition state analog bound indicates a "tight" intermediate. A striking structure homology, with significant sequence conservation, among PSP, P-type ATPases and response regulators suggests that the knowledge of the PSP reaction mechanism from the structures determined will provide insights into the reaction mechanisms of the other enzymes in this family.

Selected figure(s)

Figure 3.
Figure 3. PSP structure: (a) a ribbon diagram; (b) a topology diagram.

Figure 5.
Figure 5. Structural "snapshots" of the PSP reaction cycle in the active site. (a) The PSP reaction cycle. (b) Structure and models in the active site. (I) The apo-enzyme structure. (II) The substrate, PLS, bound structure, using mutant D11N. (III) The model of Ser bound transition state structural analogue. A Ser molecule was modeled in the AlF[3]-PSP active site. (IV) Phospho-aspartyl enzyme intermediate structural analogue. The PSP+BeF[3]^ - complex. (V) The transition state structural analogue. AlF[3]-PSP complex. (VI) The product, Pi, bound structure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 421-431) copyright 2002.

Figures were selected by the author.