PDBsum entry 2d4m

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protein links
Hydrolase PDB id
Protein chain
113 a.a. *
Waters ×147
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of apo 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)
1.85Å     R-factor:   0.162     R-free:   0.192
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
20-Oct-05     Release date:   21-Nov-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07570  (VPRT_MPMV) -  Protease
314 a.a.
113 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dUTP metabolic process   1 term 
  Biochemical function     hydrolase activity     1 term  


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.
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.