PDBsum entry 2d4l

Hydrolase

PDB id: 2d4l

Contents

Protein chain

114 a.a. *

Waters ×124

* Residue conservation analysis

PDB id:

2d4l

Name:

Hydrolase

Title:

Crystal structure of truncated in c-terminal m-pmv dutpase

Structure:

Du. Chain: a. Fragment: residues 83-234. Synonym: deoxyuridine 5'-triphosphate nucleotido hydrolase. Engineered: yes. Mutation: yes

Source:

Mason-pfizer monkey virus. Organism_taxid: 11855. Gene: gag-pro. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.70Å R-factor: 0.163 R-free: 0.179

Authors:

V.Nemeth,O.Barabas,G.B.Vertessy

Key ref:

V.Németh-Pongrácz et al. (2007). Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. Nucleic Acids Res, 35, 495-505. PubMed id: 17169987

Date:

20-Oct-05 Release date: 07-Nov-06

Protein chain

P07570  (PRO_MPMV) -  Gag-Pro polyprotein from Mason-Pfizer monkey virus

Seq: 911 a.a.

Struc: 114 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.3.4.23.- - ?????
• Enzyme class 2: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

Nucleic Acids Res 35:495-505 (2007)

PubMed id: 17169987

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.

V.Németh-Pongrácz, O.Barabás, M.Fuxreiter, I.Simon, I.Pichová, M.Rumlová, H.Zábranská, D.Svergun, M.Petoukhov, V.Harmat, E.Klement, E.Hunyadi-Gulyás, K.F.Medzihradszky, E.Kónya, B.G.Vértessy.

ABSTRACT

The homotrimeric fusion protein nucleocapsid (NC)-dUTPase combines domains that participate in RNA/DNA folding, reverse transcription, and DNA repair in Mason-Pfizer monkey betaretrovirus infected cells. The structural organization of the fusion protein remained obscured by the N- and C-terminal flexible segments of dUTPase and the linker region connecting the two domains that are invisible in electron density maps. Small-angle X-ray scattering reveals that upon oligonucleotide binding the NC domains adopt the trimeric symmetry of dUTPase. High-resolution X-ray structures together with molecular modeling indicate that fusion with NC domains dramatically alters the conformation of the flexible C-terminus by perturbing the orientation of a critical beta-strand. Consequently, the C-terminal segment is capable of double backing upon the active site of its own monomer and stabilized by non-covalent interactions formed with the N-terminal segment. This co-folding of the dUTPase terminal segments, not observable in other homologous enzymes, is due to the presence of the fused NC domain. Structural and genomic advantages of fusing the NC domain to a shortened dUTPase in betaretroviruses and the possible physiological consequences are envisaged.