PDBsum entry 1s1t

Transferase

PDB id: 1s1t

Contents

Protein chains

534 a.a. *

416 a.a. *

Ligands

PO4 ×2

UC1

Waters ×184

* Residue conservation analysis

PDB id:

1s1t

Name:

Transferase

Title:

Crystal structure of l100i mutant HIV-1 reverse transcriptase in complex with uc-781

Structure:

Reverse transcriptase. Chain: a. Fragment: p66. Synonym: HIV-1 rt. Engineered: yes. Mutation: yes. Reverse transcriptase. Chain: b. Fragment: p51.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.206 R-free: 0.274

Authors:

J.Ren,C.E.Nichols,P.P.Chamberlain,D.K.Stammers

Key ref:

J.Ren et al. (2004). Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors. J Mol Biol, 336, 569-578. PubMed id: 15095972 DOI: 10.1016/j.jmb.2003.12.055

Date:

07-Jan-04 Release date: 29-Jun-04

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 534 a.a.*

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 416 a.a.*

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

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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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: 10.1016/j.jmb.2003.12.055

J Mol Biol 336:569-578 (2004)

PubMed id: 15095972

Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors.

J.Ren, C.E.Nichols, P.P.Chamberlain, K.L.Weaver, S.A.Short, D.K.Stammers.

ABSTRACT

Leu100Ile, Val106Ala and Val108Ile are mutations in HIV-1 reverse transcriptase (RT) that are observed in the clinic and give rise to resistance to certain non-nucleoside inhibitors (NNRTIs) including the first-generation drug nevirapine. In order to investigate structural mechanisms of resistance for different NNRTI classes we have determined six crystal structures of mutant RT-inhibitor complexes. Val108 does not have direct contact with nevirapine in wild-type RT and in the RT(Val108Ile) complex the biggest change observed is at the distally positioned Tyr181 which is > 8 A from the mutation site. Thus in contrast to most NNRTI resistance mutations RT(Val108Ile) appears to act via an indirect mechanism which in this case is through alterations of the ring stacking interactions of the drug particularly with Tyr181. Shifts in side-chain and inhibitor positions compared to wild-type RT are observed in complexes of nevirapine and the second-generation NNRTI UC-781 with RT(Leu100Ile) and RT(Val106Ala), leading to perturbations in inhibitor contacts with Tyr181 and Tyr188. Such perturbations are likely to be a factor contributing to the greater loss of binding for nevirapine compared to UC-781 as, in the former case, a larger proportion of binding energy is derived from aromatic ring stacking of the inhibitor with the tyrosine side-chains. The differing resistance profiles of first and second generation NNRTIs for other drug resistance mutations in RT may also be in part due to this indirect mechanism.

Selected figure(s)

Figure 2.
Figure 2. Comparison of the NNRTI-binding sites of wild-type and mutant HIV-1 RTs. a, Leu100Ile with nevirapine. b, Leu100Ile with TNK-651. c, Leu100Ile and UC-781. The CA backbones and side-chains are shown as thin and thick bonds, coloured in orange and blue for wild-type and mutant RTs, respectively. For clarity the inhibitors and the side-chains of the corresponding mutation sites are coloured in red for wild-type and cyan for mutant RTs.

Figure 3.
Figure 3. Comparison of the NNRTI-binding sites of wild-type and mutant HIV-1 RTs with bound inhibitors. a, Val106Ala with nevirapine; b, Val106Ala with UC-781; c, Val108Ile with nevirapine. Colour coding is the same as for Figure 2.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 336, 569-578) copyright 2004.

Figures were selected by an automated process.