PDBsum entry: 1xdo

Transferase

PDB id: 1xdo

Contents

Protein chains

687 a.a. *

* Residue conservation analysis

PDB id:

1xdo

Name:

Transferase

Title:

Crystal structure of escherichia coli polyphosphate kinase

Structure:

Polyphosphate kinase. Chain: a, b. Synonym: ppk, polyphosphoric acid kinase, atp- polyphosphate phosphotransferase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ppk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.00Å R-factor: 0.255 R-free: 0.273

Authors:

Y.Zhu,W.Huang,S.S.Lee,W.Xu

Key ref:

Y.Zhu et al. (2005). Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. EMBO Rep, 6, 681-687. PubMed id: 15947782 DOI: 10.1038/sj.embor.7400448

Date:

07-Sep-04 Release date: 21-Jun-05

Protein chains

P0A7B1  (PPK_ECOLI) -  Polyphosphate kinase

Seq: 688 a.a.

Struc: 687 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.1 - Polyphosphate kinase.
• Reaction: ATP + (phosphate)(n) = ADP + (phosphate)(n+1)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (4 terms)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1038/sj.embor.7400448

EMBO Rep 6:681-687 (2005)

PubMed id: 15947782

Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis.

Y.Zhu, W.Huang, S.S.Lee, W.Xu.

ABSTRACT

Polyphosphate (polyP), a linear polymer of hundreds of orthophosphate residues, exists in all tested cells in nature, from pathogenic bacteria to mammals. In bacteria, polyP has a crucial role in stress responses and stationary-phase survival. Polyphosphate kinase (PPK) is the principal enzyme that catalyses the synthesis of polyP in bacteria. It has been shown that PPK is required for bacterial motility, biofilm formation and the production of virulence factors. PPK inhibitors may thus provide a unique therapeutic opportunity against antibiotic-resistant pathogens. Here, we report crystal structures of full-length Escherichia coli PPK and its complex with AMPPNP (beta-gamma-imidoadenosine 5-phosphate). PPK forms an interlocked dimer, with each 80 kDa monomer containing four structural domains. The PPK active site is located in a tunnel, which contains a unique ATP-binding pocket and may accommodate the translocation of synthesized polyP. The PPK structure has laid the foundation for understanding the initiation of polyP synthesis by PPK.

Selected figure(s)

Figure 2.
Figure 2 Overall structure of Escherichia coli polyphosphate kinase (PPK). (A) Structure of the PPK dimer in the asymmetric unit. The N-terminal domain of both subunits (residues 2 -106) is coloured in blue, the head domain (residues 107 -321) in green, the C-terminal domain C1 (residues 322 -502) in yellow and domain C2 (residues 503 -687) in red. The head domain of one PPK molecule (H) interacts with the C1-domain of the other PPK molecule (C1'). Each AMPPNP ( - -imidoadenosine 5-phosphate) molecule is depicted in a ball-and-stick representation, coloured in blue and magenta. (B) Structure of PPK monomer (80 kDa, 687 amino acids), viewed from the side (left) and after a 90° rotation from the side (right). Helices (h) and strands (s) are labelled consecutively from the N to C termini. All domains and AMPPNP are coloured in the same code as (A).

Figure 5.
Figure 5 ATP-binding site of polyphosphate kinase (PPK) and the chemical mechanism for PPK autophosphorylation. (A) The hydrogen-bonding network present in the PPK -AMPPNP ( - -imidoadenosine 5-phosphate) complex. The dashed lines indicate hydrogen bonds formed among phosphate groups of AMPPNP, Mg2+ and PPK active-site residues, with distances shown in angstroms. Hydrophobic contacts are indicated as radial lines around residues. The dotted line shows the distance between the -phosphorus atom of AMPPNP and the N epsilon [2] atom of PPK His 435. (B) The proposed chemical mechanism for PPK autophosphorylation.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2005, 6, 681-687) copyright 2005.

Figures were selected by an automated process.