PDBsum entry 2qb7

Hydrolase

PDB id: 2qb7

Contents

Protein chains

393 a.a. *

Ligands

PO4 ×6

ACT ×3

EDO ×4

Metals

_CO ×4

Waters ×784

* Residue conservation analysis

PDB id:

2qb7

Name:

Hydrolase

Title:

Saccharomyces cerevisiae cytosolic exopolyphosphatase, phosphate complex

Structure:

Exopolyphosphatase. Chain: a, b. Synonym: exopolypase, metaphosphatase. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c. Atcc: 204511. Gene: ppx1, yhr201c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.60Å R-factor: 0.172 R-free: 0.201

Authors:

S.A.White,E.Ugochukwu

Key ref:

E.Ugochukwu et al. (2007). The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity. J Mol Biol, 371, 1007-1021. PubMed id: 17599355 DOI: 10.1016/j.jmb.2007.05.066

Date:

16-Jun-07 Release date: 11-Dec-07

Protein chains

P38698  (PPX1_YEAST) -  Polyphosphatase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 397 a.a.

Struc: 393 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.11 - exopolyphosphatase.
• Reaction: [phosphate](n) + H2O = [phosphate](n-1) + phosphate + H⁺

[phosphate](n) + H2O = [phosphate](n-1) + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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

Key reference

DOI no: 10.1016/j.jmb.2007.05.066

J Mol Biol 371:1007-1021 (2007)

PubMed id: 17599355

The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity.

E.Ugochukwu, A.L.Lovering, O.C.Mather, T.W.Young, S.A.White.

ABSTRACT

Inorganic long-chain polyphosphate is a ubiquitous linear polymer in biology, consisting of many phosphate moieties linked by phosphoanhydride bonds. It is synthesized by polyphosphate kinase, and metabolised by a number of enzymes, including exo- and endopolyphosphatases. The Saccharomyces cerevisiae gene PPX1 encodes for a 45 kDa, metal-dependent, cytosolic exopolyphosphatase that processively cleaves the terminal phosphate group from the polyphosphate chain, until inorganic pyrophosphate is all that remains. PPX1 belongs to the DHH family of phosphoesterases, which includes: family-2 inorganic pyrophosphatases, found in Gram-positive bacteria; prune, a cyclic AMPase; and RecJ, a single-stranded DNA exonuclease. We describe the high-resolution X-ray structures of yeast PPX1, solved using the multiple isomorphous replacement with anomalous scattering (MIRAS) technique, and its complexes with phosphate (1.6 A), sulphate (1.8 A) and ATP (1.9 A). Yeast PPX1 folds into two domains, and the structures reveal a strong similarity to the family-2 inorganic pyrophosphatases, particularly in the active-site region. A large, extended channel formed at the interface of the N and C-terminal domains is lined with positively charged amino acids and represents a conduit for polyphosphate and the site of phosphate hydrolysis. Structural comparisons with the inorganic pyrophosphatases and analysis of the ligand-bound complexes lead us to propose a hydrolysis mechanism. Finally, we discuss a structural basis for substrate selectivity and processivity.

Selected figure(s)

Figure 3.
Figure 3. A TOPS diagram^62 showing the tertiary structure of S.c.-PPX1. Secondary structure elements are labelled as in Figure 1. Loop L-M forms the hinge linking the N and C-terminal domains.

Figure 8.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 1007-1021) copyright 2007.

Figures were selected by an automated process.