PDBsum entry 4bac

Transferase/DNA

PDB id: 4bac

Contents

Protein chains

368 a.a.

184 a.a.

DNA/RNA

Metals

_MG ×2

_ZN

Waters ×3

PDB id:

4bac

Name:

Transferase/DNA

Title:

Prototype foamy virus strand transfer complexes on product DNA

Structure:

Integrase. Chain: a, b. Synonym: in, p42in. Engineered: yes. 5'-d( Ap Tp Tp Gp Tp Cp Ap Tp Gp Gp Ap Ap Tp Tp Tp Tp Gp Tp Ap)-3'. Chain: c. Engineered: yes. DNA (38-mer).

Source:

Human spumaretrovirus. Organism_taxid: 11963. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

3.26Å R-factor: 0.187 R-free: 0.226

Authors:

Z.Yin,M.Lapkouski,W.Yang,R.Craigie

Key ref:

Z.Yin et al. (2012). Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration. Protein Sci, 21, 1849-1857. PubMed id: 23011895

Date:

12-Sep-12 Release date: 10-Oct-12

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.

DNA/RNA chains

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

T-A-C-A-A-A-A-T-T-C-C-A-T-G-A-C-A-G-T-A-C-G-A-T-C-C-G-T-C-T-T-G-A 33 bases

C-C-A-A-G-A-C-G-G-A-T-C 12 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

Protein Sci 21:1849-1857 (2012)

PubMed id: 23011895

Assembly of prototype foamy virus strand transfer complexes on product DNA bypassing catalysis of integration.

Z.Yin, M.Lapkouski, W.Yang, R.Craigie.

ABSTRACT

Integrase is the key enzyme that mediates integration of retroviral DNA into cellular DNA which is essential for viral replication. Inhibitors of HIV-1 that target integrase recognize the nucleoprotein complexes formed by integrase and viral DNA substrate (intasomes) rather than the free enzyme. Atomic resolution structures of HIV-1 intasomes are therefore required to understand the mechanisms of inhibition and drug resistance. To date, prototype foamy virus (PFV) is the only retrovirus for which such structures have been determined. We show that PFV strand transfer complexes (STC) can be assembled on product DNA without going through the normal forward reaction pathway. The finding that a retroviral STC can be assembled in this way may provide a powerful tool to alleviate the obstacles that impede structural studies of nucleoprotein intermediates in HIV-1 DNA integration.