PDBsum entry 7lrm

Transferase/DNA

PDB id: 7lrm

Contents

Protein chains

553 a.a.

415 a.a.

DNA/RNA

Ligands

GLC-FRU ×2

SO4 ×2

GOL ×12

DCP ×2

Metals

_CA ×2

Waters ×150

PDB id:

7lrm

Name:

Transferase/DNA

Title:

Structure of HIV-1 reverse transcriptase in complex with DNA, dctp, and ca(2+) ion

Structure:

Reverse transcriptase p66. Chain: a, c. Engineered: yes. Mutation: yes. Reverse transcriptase p51. Chain: b, d. Engineered: yes. Mutation: yes. DNA/RNA (38-mer).

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

3.14Å R-factor: 0.196 R-free: 0.244

Authors:

A.Hoang,F.X.Ruiz,E.Arnold

Key ref:

F.X.Ruiz et al. Structural basis of HIV inhibition by l-Nucleotides: opportunities for drug development and repurposing. To be published, . PubMed id: 35218925

Date:

16-Feb-21 Release date: 23-Feb-22

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: 553 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: 415 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

T-G-C-OMC-C-OMC-C-C-C-T-T-C-G-G-T-G-C-T-T-T-G-C-A-C-C-G-A-A-G-G-G-G-G-G-G 35 bases

T-G-C-OMC-C-OMC-C-C-C-T-T-C-G-G-T-G-C-T-T-T-G-C-A-C-C-G-A-A-G-G-G-G-G-G-G 35 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