PDBsum entry 3oye

Recombination,viral protein/DNA

PDB id: 3oye

Contents

Protein chains

368 a.a. *

184 a.a. *

DNA/RNA

Ligands

SO4 ×2

GOL ×4

NH4

ZYY

Metals

_MG ×3

_ZN

Waters ×217

* Residue conservation analysis

PDB id:

3oye

Name:

Recombination,viral protein/DNA

Title:

Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti compound2

Structure:

Pfv integrase. Chain: a, b. Fragment: unp residues 752 to 1143. Synonym: p42in. Engineered: yes. DNA (5'- d( Ap Tp Tp Gp Tp Cp Ap Tp Gp Gp Ap Ap Tp Tp Tp Cp Gp Cp A)-3'). Chain: c. Engineered: yes.

Source:

Human spumaretrovirus. Sfvcpz(hu). Organism_taxid: 11963. Strain: hsrv2. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: donor DNA non-transferred strand.

Resolution:

2.74Å R-factor: 0.205 R-free: 0.234

Authors:

S.Hare,P.Cherepanov

Key ref:

S.Hare et al. (2010). Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proc Natl Acad Sci U S A, 107, 20057-20062. PubMed id: 21030679

Date:

23-Sep-10 Release date: 17-Nov-10

Protein chain

P14350  (POL_FOAMV) -  Pro-Pol polyprotein from Human spumaretrovirus

Seq: 1143 a.a.

Struc: 368 a.a.*

Protein chain

P14350  (POL_FOAMV) -  Pro-Pol polyprotein from Human spumaretrovirus

Seq: 1143 a.a.

Struc: 184 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

A-T-T-G-T-C-A-T-G-G-A-A-T-T-T-C-G-C-A 19 bases

T-G-C-G-A-A-A-T-T-C-C-A-T-G-A-C-A 17 bases

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 3: Chains A, B: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: Chains A, B: E.C.3.1.-.-
• Enzyme class 6: Chains A, B: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: Chains A, B: E.C.3.4.23.- - ?????

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

Proc Natl Acad Sci U S A 107:20057-20062 (2010)

PubMed id: 21030679

Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.

S.Hare, A.M.Vos, R.F.Clayton, J.W.Thuring, M.D.Cummings, P.Cherepanov.

ABSTRACT

No abstract given.