PDBsum entry: 1dlo

Nucleotidyltransferase

PDB id: 1dlo

Contents

Protein chains

556 a.a. *

415 a.a. *

* Residue conservation analysis

PDB id:

1dlo

Name:

Nucleotidyltransferase

Title:

Human immunodeficiency virus type 1

Structure:

Human immunodeficiency virus type 1 reverse transcriptase. Chain: a. Synonym: HIV-1 rt. Engineered: yes. Mutation: yes. Human immunodeficiency virus type 1 reverse transcriptase. Chain: b.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10 isolate. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.249 R-free: 0.336

Authors:

Y.Hsiou,J.Ding,K.Das,S.Hughes,E.Arnold

Key ref:

Y.Hsiou et al. (1996). Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure, 4, 853-860. PubMed id: 8805568 DOI: 10.1016/S0969-2126(96)00091-3

Date:

17-Apr-96 Release date: 01-Aug-96

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein

Seq: 1447 a.a.

Struc: 556 a.a.*

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein

Seq: 1447 a.a.

Struc: 415 a.a.*

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

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 2: Chains A, B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
• Enzyme class 3: 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 4: Chains A, B: E.C.3.1.26.13 - Retroviral ribonuclease H.
• Enzyme class 5: 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

 Gene Ontology (GO) functional annotation 

• Biological process: RNA-dependent DNA replication (1 term)
• Biochemical function: nucleic acid binding (4 terms)

reference

DOI no: 10.1016/S0969-2126(96)00091-3

Structure 4:853-860 (1996)

PubMed id: 8805568

Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms.

Y.Hsiou, J.Ding, K.Das, A.D.Clark, S.H.Hughes, E.Arnold.

ABSTRACT

BACKGROUND: HIV-1 reverse transcriptase (RT) is a major target for anti-HIV drugs. A considerable amount of information about the structure of RT is available, both unliganded and in complex with template-primer or non-nucleoside RT inhibitors (NNRTIs). But significant conformational differences in the p66 polymerase domain among the unliganded structures have complicated the interpretation of these data, leading to different proposals for the mechanisms of polymerization and inhibition. RESULTS: We report the structure of an unliganded RT at 2.7 A resolution, crystallized in space group C2 with a crystal packing similar to that of the RT-NNRTI complexes. The p66 thumb subdomain is folded into the DNA-binding cleft. Comparison of the unliganded RT structures with the DNA-bound RT and the NNRTI-bound RT structures reveals that the p66 thumb subdomain can exhibit two different upright conformations. In the DNA-bound RT, the p66 thumb subdomain adopts an upright position that can be described as resulting from a rigid-body rotation of the p66 thumb along the "thumb's knuckle' located near residues Trp239 (in strand beta 14) and Val317 (in beta 15) compared with the thumb position in the unliganded RT structure. NNRTI binding induces an additional hinge movement of the p66 thumb near the thumb's knuckle, causing the p66 thumb to adopt a configuration that is even more extended than in the DNA-bound RT structure. CONCLUSIONS: The p66 thumb subdomain is extremely flexible. NNRTI binding induces both short-range and long-range structural distortions in several domains of RT, which are expected to alter the position and conformation of the template-primer. These changes may account for the inhibition of polymerization and the alteration of the cleavage specificity of RNase H by NNRTI binding.

Selected figure(s)

Figure 3.
Figure 3. Superposition of (a) unliganded RT and RT–DNA–Fab complex and (b) unliganded RT and RT–α-APA (α-anilinophenylacetamide) complex based on 89 Cα atoms in the p66 palm subdomain, including the β6–β10–β9 region. The unliganded RT is shown in red, RT–α-APA in blue, and RT–DNA–Fab in green. A comparison of the two superpositions reveals that NNRTI binding appears to be accompanied by a long-range distortion that is coupled with a hinge motion (indicated by curved arrows) between the β6–β10–β9 and β12–β13–β14 sheets at the p66 palm subdomain (within the circle). The different positions of the thumb in different HIV-1 RT structures supports the idea that this subdomain could play a role during polymerization. Figure 3. Superposition of (a) unliganded RT and RT–DNA–Fab complex and (b) unliganded RT and RT–α-APA (α-anilinophenylacetamide) complex based on 89 Cα atoms in the p66 palm subdomain, including the β6–β10–β9 region. The unliganded RT is shown in red, RT–α-APA in blue, and RT–DNA–Fab in green. A comparison of the two superpositions reveals that NNRTI binding appears to be accompanied by a long-range distortion that is coupled with a hinge motion (indicated by curved arrows) between the β6–β10–β9 and β12–β13–β14 sheets at the p66 palm subdomain (within the circle). The different positions of the thumb in different HIV-1 RT structures supports the idea that this subdomain could play a role during polymerization.

Figure 4.
Figure 4. Stereoview of a portion of a (2mF[obs]–F[calc]) difference Fourier map at the p66 connection subdomain, at 2.7 å resolution. The phases were computed from the current atomic model and the map is contoured at 1.4σ. The side chain and the carboxyl groups are well defined in the electron density map. Figure 4. Stereoview of a portion of a (2mF[obs]–F[calc]) difference Fourier map at the p66 connection subdomain, at 2.7 å resolution. The phases were computed from the current atomic model and the map is contoured at 1.4σ. The side chain and the carboxyl groups are well defined in the electron density map.

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 853-860) copyright 1996.

Figures were selected by the author.