PDBsum entry 3os2

Recombination/DNA

PDB id: 3os2

Contents

Protein chains

365 a.a. *

163 a.a. *

DNA/RNA

Ligands

SO4

Metals

_ZN

* Residue conservation analysis

PDB id:

3os2

Name:

Recombination/DNA

Title:

Pfv target capture complex (tcc) at 3.32 a resolution

Structure:

Integrase. Chain: a, b. Synonym: pr125pol, protease/reverse transcriptase/ribonuclease h, p87pro-rt-rnaseh, protease/reverse transcriptase, p65pro-rt, ribonuclease h, rnase h, integrase, in, 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.

Source:

Human spumaretrovirus. Organism_taxid: 11963. Strain: pfv. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic oligonucleotide. Other_details: synthetic oligonucleotide

Resolution:

3.32Å R-factor: 0.225 R-free: 0.260

Authors:

G.N.Maertens,S.Hare,P.Cherepanov

Key ref:

G.N.Maertens et al. (2010). The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature, 468, 326-329. PubMed id: 21068843

Date:

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

Protein chain

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

Seq: 1143 a.a.

Struc: 365 a.a.*

Protein chain

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

Seq: 1143 a.a.

Struc: 163 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

C-A-C-G-T-G-C-T-A-G-C-A-C-G-T-G 16 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

Nature 468:326-329 (2010)

PubMed id: 21068843

The mechanism of retroviral integration from X-ray structures of its key intermediates.

G.N.Maertens, S.Hare, P.Cherepanov.

ABSTRACT

To establish productive infection, a retrovirus must insert a DNA replica of its genome into host cell chromosomal DNA. This process is operated by the intasome, a nucleoprotein complex composed of an integrase tetramer (IN) assembled on the viral DNA ends. The intasome engages chromosomal DNA within a target capture complex to carry out strand transfer, irreversibly joining the viral and cellular DNA molecules. Although several intasome/transpososome structures from the DDE(D) recombinase superfamily have been reported, the mechanics of target DNA capture and strand transfer by these enzymes remained unclear. Here we report crystal structures of the intasome from prototype foamy virus in complex with target DNA, elucidating the pre-integration target DNA capture and post-catalytic strand transfer intermediates of the retroviral integration process. The cleft between IN dimers within the intasome accommodates chromosomal DNA in a severely bent conformation, allowing widely spaced IN active sites to access the scissile phosphodiester bonds. Our results resolve the structural basis for retroviral DNA integration and provide a framework for the design of INs with altered target sequences.