PDBsum entry 1b6t

Transferase

PDB id: 1b6t

Contents

Protein chains

157 a.a. *

Ligands

SO4 ×3

COD

Waters ×322

* Residue conservation analysis

PDB id:

1b6t

Name:

Transferase

Title:

Phosphopantetheine adenylyltransferase in complex with 3'-dephospho- coa from escherichia coli

Structure:

Protein (phosphopantetheine adenylyltransferase). Chain: a, b. Synonym: ppat, kdtb. Ec: 2.7.7.3

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.80Å R-factor: 0.205 R-free: 0.235

Authors:

T.Izard

Key ref:

T.Izard and A.Geerlof (1999). The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity. EMBO J, 18, 2021-2030. PubMed id: 10205156 DOI: 10.1093/emboj/18.8.2021

Date:

18-Jan-99 Release date: 19-Apr-00

Protein chains

P0A6I6  (COAD_ECOLI) -  Phosphopantetheine adenylyltransferase from Escherichia coli (strain K12)

Seq: 159 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.3 - pantetheine-phosphate adenylyltransferase.
• Pathway: Coenzyme A Biosynthesis (late stages)
• Reaction: (R)-4'-phosphopantetheine + ATP + H⁺ = 3'-dephospho-CoA + diphosphate

(R)-4'-phosphopantetheine + ATP (Bound ligand (Het Group name = COD) matches with 56.25% similarity) + H(+) = 3'-dephospho-CoA + diphosphate

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

Added reference

DOI no: 10.1093/emboj/18.8.2021

EMBO J 18:2021-2030 (1999)

PubMed id: 10205156

The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity.

T.Izard, A.Geerlof.

ABSTRACT

Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in bacteria that catalyses a rate-limiting step in coenzyme A (CoA) biosynthesis, by transferring an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA). Each phosphopantetheine adenylyltransferase (PPAT) subunit displays a dinucleotide-binding fold that is structurally similar to that in class I aminoacyl-tRNA synthetases. Superposition of bound adenylyl moieties from dPCoA in PPAT and ATP in aminoacyl-tRNA synthetases suggests nucleophilic attack by the 4'-phosphopantetheine on the alpha-phosphate of ATP. The proposed catalytic mechanism implicates transition state stabilization by PPAT without involving functional groups of the enzyme in a chemical sense in the reaction. The crystal structure of the enzyme from Escherichia coli in complex with dPCoA shows that binding at one site causes a vice-like movement of active site residues lining the active site surface. The mode of enzyme product formation is highly concerted, with only one trimer of the PPAT hexamer showing evidence of dPCoA binding. The homologous active site attachment of ATP and the structural distribution of predicted sequence-binding motifs in PPAT classify the enzyme as belonging to the nucleotidyltransferase superfamily.

Selected figure(s)

Figure 1.
Figure 1 The penultimate step in the CoA biosynthetic pathway. PPAT reversibly catalyses the adenylation by ATP of 4'-phosphopantetheine, forming 3'-dephospho-CoA and pyrophosphate.

Figure 3.
Figure 3 The PPAT hexamer. (A) Electrostatic surface potential (using the program GRASP; Nicholls et al., 1991) of the PPAT hexamer along the triad (red, negative; blue, positive; white, uncharged). The diameter along the 3-fold axis is 75 Å, with a channel across the entire hexamer with a diameter of at least 10 Å. The substrates and products must enter through this cavity to bind to the active site of the protein. Space-filling representations (using the program RASTER3D; Bacon and Anderson, 1988; Merritt and Murphy, 1994) looking down (B) the triad and (C) the dyad. Each of the six subunits is coloured differently.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 2021-2030) copyright 1999.

Figures were selected by an automated process.