PDBsum entry 3v81

Transferase/DNA

PDB id: 3v81

Contents

Protein chains

555 a.a.

412 a.a.

DNA/RNA

Ligands

NVP ×2

PDB id:

3v81

Name:

Transferase/DNA

Title:

Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and the nonnucleoside inhibitor nevirapine

Structure:

HIV-1 reverse transcriptase p66 subunit. Chain: a, c. Fragment: unp residues 600-1153. Engineered: yes. Mutation: yes. HIV-1 reverse transcriptase p51 subunit. Chain: b, d. Fragment: unp residues 600-1027. Engineered: yes.

Source:

Human immunodeficiency virus type 1 bh10. HIV-1. Organism_taxid: 11678. Strain: bh10 isolate. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthesized.

Resolution:

2.85Å R-factor: 0.252 R-free: 0.298

Authors:

K.Das,S.E.Martinez,E.Arnold

Key ref:

K.Das et al. (2012). HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Biol, 19, 253-259. PubMed id: 22266819

Date:

22-Dec-11 Release date: 18-Jan-12

Protein chains

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 555 a.a.*

Protein chains

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 412 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

A-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C-T-G 20 bases

C-A-G-T-C-C-C-T-G-T-T-C-G-G-MRG-C-G-C-C-ATM 20 bases

A-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C-T-G 20 bases

C-A-G-T-C-C-C-T-G-T-T-C-G-G-MRG-C-G-C-C-ATM 20 bases

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B, C, D: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C, D: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B, C, D: E.C.3.1.-.-
• Enzyme class 5: Chains A, B, C, D: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: Chains A, B, C, D: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B, C, D: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

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

Nat Struct Biol 19:253-259 (2012)

PubMed id: 22266819

HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.

K.Das, S.E.Martinez, J.D.Bauman, E.Arnold.

ABSTRACT

No abstract given.