PDBsum entry: 1pkj

Hydrolase

PDB id: 1pkj

Contents

Protein chains

180 a.a. *

Ligands

EDO ×2

DUT

Waters ×255

* Residue conservation analysis

PDB id:

1pkj

Name:

Hydrolase

Title:

Structural basis for recognition and catalysis by the bifunc dctp deaminase and dutpase from methanococcus jannaschii

Structure:

Bifunctional deaminase/diphosphatase. Chain: a, b. Synonym: mjdcd-dut, dcd/dut. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: mj0430. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.10Å R-factor: 0.193 R-free: 0.233

Authors:

J.L.Huffman,H.Li,R.H.White,J.A.Tainer

Key ref:

J.L.Huffman et al. (2003). Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii. J Mol Biol, 331, 885-896. PubMed id: 12909016 DOI: 10.1016/S0022-2836(03)00789-7

Date:

05-Jun-03 Release date: 23-Sep-03

Protein chains

Q57872  (DCD_METJA) -  dCTP deaminase, dUMP-forming

Seq: 204 a.a.

Struc: 180 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.30 - dCTP deaminase (dUMP-forming).
• Reaction: dCTP + 2 H₂O = dUMP + diphosphate + NH₃

dCTP (Bound ligand (Het Group name = DUT) matches with 93.10% similarity) + 2 × H(2)O = dUMP + diphosphate + NH(3)

• Cofactor: Magnesium

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

 Gene Ontology (GO) functional annotation 

• Biological process: nucleotide metabolic process (3 terms)
• Biochemical function: hydrolase activity (3 terms)

reference

DOI no: 10.1016/S0022-2836(03)00789-7

J Mol Biol 331:885-896 (2003)

PubMed id: 12909016

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii.

J.L.Huffman, H.Li, R.H.White, J.A.Tainer.

ABSTRACT

Potentially mutagenic uracil-containing nucleotide intermediates are generated by deamination of dCTP, either spontaneously or enzymatically as the first step in the conversion of dCTP to dTTP. dUTPases convert dUTP to dUMP, thus avoiding the misincorporation of dUTP into DNA and creating the substrate for the next enzyme in the dTTP synthetic pathway, thymidylate synthase. Although dCTP deaminase and dUTPase activities are usually found in separate but homologous enzymes, the hyperthermophile Methanococcus jannaschii has an enzyme, DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities. DCD-DUT has highest activity on dCTP, followed by dUTP, and dTTP inhibits both the deaminase and pyrophosphatase activities. To help clarify structure-function relationships for DCD-DUT, we have determined the crystal structure of the wild-type DCD-DUT protein in its apo form to 1.42A and structures of DCD-DUT in complex with dCTP and dUTP to resolutions of 1.77A and 2.10A, respectively. To gain insights into substrate interactions, we complemented analyses of the experimentally defined weak density for nucleotides with automated docking experiments using dCTP, dUTP, and dTTP. DCD-DUT is a hexamer, unlike the homologous dUTPases, and its subunits contain several insertions and substitutions different from the dUTPase beta barrel core that likely contribute to dCTP specificity and deamination. These first structures of a dCTP deaminase reveal a probable role for an unstructured C-terminal region different from that of the dUTPases and possible mechanisms for both bifunctional enzyme activity and feedback inhibition by dTTP.

Selected figure(s)

Figure 7.
Figure 7. Proposed mechanism for DCD-DUT dCTP deamination.

Figure 8.
Figure 8. Docked DCD-DUT:dTTP inhibitory complex. (A) Interactions with the thymidine base, including Ile134, Phe138, and Ile142. (B) Repositioning of the sugar-phosphate moiety due to the proposed altered base conformation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 885-896) copyright 2003.

Figures were selected by an automated process.