PDBsum entry 1n6q

Transferase/immune system/DNA

PDB id: 1n6q

Contents

Protein chains

558 a.a. *

429 a.a. *

211 a.a. *

225 a.a. *

DNA/RNA

Metals

_MG ×2

Waters ×2

* Residue conservation analysis

PDB id:

1n6q

Name:

Transferase/immune system/DNA

Title:

HIV-1 reverse transcriptase crosslinked to pre-translocation aztmp- terminated DNA (complex n)

Structure:

5'-d( Ap T Gp Cp Ap Tp Gp Gp Cp Gp Cp Cp Cp Gp Ap Ap Cp Ap Gp Gp Gp Ap Cp Tp Gp Tp G)-3'. Chain: t. Engineered: yes. Other_details: DNA template. 5'-d( A Cp Ap Gp Tp Cp Cp Cp Tp Gp Tp Tp Cp Gp Gp (Mrg) p Cp Gp Cp Cp Ap (Atm))-3'. Chain: p. Engineered: yes.

Source:

Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.

Biol. unit:

Hexamer (from PQS)

Resolution:

3.00Å R-factor: 0.247 R-free: 0.284

Authors:

S.G.Sarafianos,A.D.Clark Jr.,K.Das,S.Tuske,J.J.Birktoft, I.Ilankumaran,A.R.Ramesha,J.M.Sayer,D.M.Jerina,P.L.Boyer,S.H.Hughes, E.Arnold

Key ref:

S.G.Sarafianos et al. (2002). Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA. EMBO J, 21, 6614-6624. PubMed id: 12456667 DOI: 10.1093/emboj/cdf637

Date:

11-Nov-02 Release date: 14-Jan-03

Protein chain

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

Seq: 1447 a.a.

Struc: 558 a.a.*

Protein chain

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

Seq: 1447 a.a.

Struc: 429 a.a.*

Protein chain

I6L991  (I6L991_MOUSE) -  Ig-like domain-containing protein from Mus musculus

Seq: 234 a.a.

Struc: 211 a.a.*

Protein chain

P01868  (IGHG1_MOUSE) -  Ig gamma-1 chain C region secreted form from Mus musculus

Seq: 324 a.a.

Struc: 225 a.a.*

* PDB and UniProt seqs differ at 13 residue positions (black crosses)

DNA/RNA chains

G-C-A-T-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C-T-G 23 bases

C-A-G-T-C-C-C-T-G-T-T-C-G-G-MRG-C-G-C-C-A-ATM 21 bases

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: 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 3: 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 4: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: 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: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B: 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

DOI no: 10.1093/emboj/cdf637

EMBO J 21:6614-6624 (2002)

PubMed id: 12456667

Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.

S.G.Sarafianos, A.D.Clark, K.Das, S.Tuske, J.J.Birktoft, P.Ilankumaran, A.R.Ramesha, J.M.Sayer, D.M.Jerina, P.L.Boyer, S.H.Hughes, E.Arnold.

ABSTRACT

AZT (3'-azido-3'-deoxythymidine) resistance involves the enhanced excision of AZTMP from the end of the primer strand by HIV-1 reverse transcriptase. This reaction can occur when an AZTMP-terminated primer is bound at the nucleotide-binding site (pre-translocation complex N) but not at the 'priming' site (post-translocation complex P). We determined the crystal structures of N and P complexes at 3.0 and 3.1 A resolution. These structures provide insight into the structural basis of AZTMP excision and the mechanism of translocation. Docking of a dNTP in the P complex structure suggests steric crowding in forming a stable ternary complex that should increase the relative amount of the N complex, which is the substrate for excision. Structural differences between complexes N and P suggest that the conserved YMDD loop is involved in translocation, acting as a springboard that helps to propel the primer terminus from the N to the P site after dNMP incorporation.

Selected figure(s)

Figure 5.
Figure 5 (A) Ribbon representation of superposed polymerase active sites (same basis of superposition as used for Figure 4) of complex N and HIV-1 RT/DNA/dNTP ternary complex [RT(ter)−ddNMP−dTTP complex] (Huang et al., 1998); PDB code 1RTD. Color scheme: side chains of complex N (cyan), primer strand of complex N (magenta), incoming dNTP of the ternary complex (yellow), metals A and B in the ternary complex (yellow). In complex N, the corresponding metals (A' and B') are either not seen in the structure and may have been released together with PPi (A'), or are observed (Figure 3) at a position shifted by 4.7 Å (metal B'). (B) Superposition of polymerase active sites of the non-terminated [RT(P)−dNMP, green] (Ding et al., 1998; PDB code 2HMI) and AZTMP-terminated P complex [RT(P)−AZTMP, white]. The main structural difference is in the inclination of the terminal nucleotide. (C) Superposition of the polymerase active sites (aligned using p66 residues 107−112 and 155−215) of complex P (in white) on the RT(ter)−ddNMP/dTTP ternary complex (in cyan) (Huang et al., 1998); PDB code 1RTD. The ternary complex YMDD loop is displaced 1.0 Å from its position in the P complex. Steric conflicts (in red) are mostly between the C5' of the incoming dNTP and the side chain of Asp185.

Figure 8.
Figure 8 Schematic relationships among events that affect excision-based NRTI resistance (dNTP binding, translocation, excision). Factors that affect any stage will affect the overall equilibrium. X is an NRTI (red), A is ATP (orange) and dNTP (cyan) is the cognate nucleotide triphosphate.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 6614-6624) copyright 2002.

Figures were selected by an automated process.