PDBsum entry 2o1c

Hydrolase

PDB id: 2o1c

Contents

Protein chains

147 a.a. *

Ligands

SO4 ×4

PPV ×3

Waters ×611

* Residue conservation analysis

PDB id:

2o1c

Name:

Hydrolase

Title:

Structure of the e. Coli dihydroneopterin triphosphate pyrophosphohydrolase

Structure:

Datp pyrophosphohydrolase. Chain: a, b, c, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: hb101. Gene: nudb, ntpa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.229 R-free: 0.289

Authors:

S.B.Gabelli,M.A.Bianchet,L.M.Amzel

Key ref:

S.B.Gabelli et al. (2007). Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis. Structure, 15, 1014-1022. PubMed id: 17698004 DOI: 10.1016/j.str.2007.06.018

Date:

28-Nov-06 Release date: 28-Aug-07

Protein chains

P0AFC0  (NUDB_ECOLI) -  Dihydroneopterin triphosphate diphosphatase from Escherichia coli (strain K12)

Seq: 150 a.a.

Struc: 147 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.67 - dihydroneopterin triphosphate diphosphatase.
• Reaction: 7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + diphosphate + H⁺

7,8-dihydroneopterin 3'-triphosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + diphosphate (Bound ligand (Het Group name = PPV) corresponds exactly) + H(+)

• Cofactor: Mg(2+)

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

Key reference

DOI no: 10.1016/j.str.2007.06.018

Structure 15:1014-1022 (2007)

PubMed id: 17698004

Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis.

S.B.Gabelli, M.A.Bianchet, W.Xu, C.A.Dunn, Z.D.Niu, L.M.Amzel, M.J.Bessman.

ABSTRACT

Nudix hydrolases are a superfamily of pyrophosphatases, most of which are involved in clearing the cell of potentially deleterious metabolites and in preventing the accumulation of metabolic intermediates. We determined that the product of the orf17 gene of Escherichia coli, a Nudix NTP hydrolase, catalyzes the hydrolytic release of pyrophosphate from dihydroneopterin triphosphate, the committed step of folate synthesis in bacteria. That this dihydroneopterin hydrolase (DHNTPase) is indeed a key enzyme in the folate pathway was confirmed in vivo: knockout of this gene in E. coli leads to a marked reduction in folate synthesis that is completely restored by a plasmid carrying the gene. We also determined the crystal structure of this enzyme using data to 1.8 A resolution and studied the kinetics of the reaction. These results provide insight into the structural bases for catalysis and substrate specificity in this enzyme and allow the definition of the dihydroneopterin triphosphate pyrophosphatase family of Nudix enzymes.

Selected figure(s)

Figure 2.
Figure 2. Structure of the E. coli Dihydroneopterin Pyrophosphatase
(A) Ribbon diagram of the structure of DHNTPase in complex with its product, pyrophosphate. Residues of the Nudix signature sequence, Arg-29 and Glu-117, are shown as green sticks. The secondary structural elements are labeled L for loops, β for strands, and α for helices.
(B) Ribbon diagram of the overlap of monomers A, B, and C (turquoise, cornflower blue, and blue, respectively) with their pyrophosphate and sulfate molecules.
(C) Molecular surface of the complex structure (monomer A, closed).
(D) Ribbon diagram of the overlap of monomer A (complex structure; turquoise) and monomer D (ligand-free structure, open; orange-red).
(E) Molecular surface of the ligand-free structure (open).

Figure 3.
Figure 3. Interactions of the Signature Sequence Nudix Residues of DHNTPase
(Left) Hydrogen-bonding pattern of the conserved residues (orange dashes) and recognition of the pyrophosphate inhibitor as observed in the native complex structure (monomers A, B, and C). (Right) Recognition of the pyrophosphate as observed in the complex in the presence of SmCl[3]. A 2F[o] − F[c] electron density map of the metal and pyrophosphate is shown contoured at 1.2σ.

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1014-1022) copyright 2007.

Figures were selected by an automated process.