PDBsum entry 2hmi

Immune system/DNA

PDB id: 2hmi

Contents

Protein chains

558 a.a. *

430 a.a. *

214 a.a. *

220 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

2hmi

Name:

Immune system/DNA

Title:

HIV-1 reverse transcriptase/fragment of fab 28/DNA complex

Structure:

DNA (5'- d( Ap Tp Gp Gp Cp Gp Cp Cp Cp Gp Ap Ap Cp Ap Gp Gp Gp Ap C)-3'). Chain: e. Engineered: yes. DNA (5'- d( Gp Tp Cp Cp Cp Tp Gp Tp Tp Cp Gp Gp Gp Cp Gp Cp Cp A)-3'). Chain: f. Engineered: yes. Subunit of v-1 reverse transcriptase.

Source:

Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10 isolate. Atcc: atcc 1065288. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.80Å R-factor: 0.271 R-free: 0.352

Authors:

J.Ding,E.Arnold

Key ref:

J.Ding et al. (1998). Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution. J Mol Biol, 284, 1095-1111. PubMed id: 9837729 DOI: 10.1006/jmbi.1998.2208

Date:

10-Apr-98 Release date: 14-Oct-98

Supersedes:

1hmi

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: 430 a.a.*

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

Protein chain

No UniProt id for this chain

Struc: 220 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

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

G-T-C-C-C-T-G-T-T-C-G-G-G-C-G-C-C-A 18 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.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 7: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 8: 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: 10.1006/jmbi.1998.2208

J Mol Biol 284:1095-1111 (1998)

PubMed id: 9837729

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.

J.Ding, K.Das, Y.Hsiou, S.G.Sarafianos, A.D.Clark, A.Jacobo-Molina, C.Tantillo, S.H.Hughes, E.Arnold.

ABSTRACT

The structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexed with a 19-mer/18-mer double-stranded DNA template-primer (dsDNA) and the Fab fragment of monoclonal antibody 28 (Fab28) has been refined at 2.8 A resolution. The structures of the polymerase active site and neighboring regions are described in detail and a number of novel insights into mechanisms of polymerase catalysis and drug inhibition are presented. The three catalytically essential amino acid residues (Asp110, Asp185, and Asp186) are located close to the 3' terminus of the primer strand. Observation of a hydrogen bond between the 3'-OH of the primer terminus and the side-chain of Asp185 suggests that the carboxylate of Asp185 could act as a general base in initiating the nucleophilic attack during polymerization. Nearly all of the close protein-DNA interactions involve atoms of the sugar-phosphate backbone of the nucleic acid. However, the phenoxyl side-chain of Tyr183, which is part of the conserved YMDD motif, has hydrogen-bonding interactions with nucleotide bases of the second duplex base-pair and is predicted to have at least one hydrogen bond with all Watson-Crick base-pairs at this position. Comparison of the structure of the active site region in the HIV-1 RT/dsDNA complex with all other HIV-1 RT structures suggests that template-primer binding is accompanied by significant conformational changes of the YMDD motif that may be relevant for mechanisms of both polymerization and inhibition by non-nucleoside inhibitors. Interactions of the "primer grip" (the beta12-beta13 hairpin) with the 3' terminus of the primer strand primarily involve the main-chain atoms of Met230 and Gly231 and the primer terminal phosphate. Alternative positions of the primer grip observed in different HIV-1 RT structures may be related to conformational changes that normally occur during DNA polymerization and translocation. In the vicinity of the polymerase active site, there are a number of aromatic residues that are involved in energetically favorable pi-pi interactions and may be involved in the transitions between different stages of the catalytic process. The protein structural elements primarily responsible for precise positioning of the template-primer (including the primer grip, template grip, and helices alphaH and alphaI of the p66 thumb) can be thought of functioning as a "translocation track" that guides the relative movement of nucleic acid and protein during polymerization.

Selected figure(s)

Figure 1.
Figure 1. Ribbon [Carson 1987] diagram showing the overall structure of the HIV-1 RT/dsDNA/Fab28 complex. The subdomains of the p66 and p51 subunits of HIV-1 RT are colored as follows: fingers, blue; palm, red; thumb, green; connection, yellow; and RNase H, orange. The bound dsDNA is shown with the template strand as a dark gray ribbon and the primer strand as a light gray ribbon; base-pairs are represented by bars. The monoclonal antibody fragment Fab28 is shown with the light chain in light gray and the heavy chain in dark gray.

Figure 3.
Figure 3. (a) Structure of the polymerase active site region of HIV-1 RT including the primer grip. Secondary structural elements of the p66 palm subdomain are shown as red ribbons. The three catalytically essential aspartic acid residues (Asp110, Asp185, and Asp186) are shown with cyan side-chains. Tyr183 and Met184, which form part of the conserved YMDD motif, are shown with gold side-chains. Amino acid residues at the primer grip are shown in green. The dsDNA is shown with the template strand in dark gray and the primer strand in light gray. (b) A schematic diagram showing interactions between the 3′-terminal nucleotide of the primer strand (Pri1) and amino acid residues at the polymerase active site, with selected distances given in Å. Hydrogen-bonding interactions between the side-chain O^δ1 atom of Asp185 and the 3′-OH of Pri1, and between the amide nitrogen atom of Met230 of the primer grip and the phosphate oxygen atom of Pri1 are indicated by heavy lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 1095-1111) copyright 1998.

Figures were selected by an automated process.