4DG1

Crystal structure of HIV-1 reverse transcriptase (RT) with polymorphism mutation K172A and K173A

DOI: 10.2210/pdb4DG1/pdb

Classification: TRANSFERASE
Organism(s): Human immunodeficiency virus type 1 BH10
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-01-24 Released: 2012-06-20
Deposition Author(s): Tu, X., Kirby, K.A., Marchand, B., Sarafianos, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.247
R-Value Work: 0.232
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

HIV-1 Reverse Transcriptase (RT) Polymorphism 172K Suppresses the Effect of Clinically Relevant Drug Resistance Mutations to Both Nucleoside and Non-nucleoside RT Inhibitors.

Hachiya, A., Marchand, B., Kirby, K.A., Michailidis, E., Tu, X., Palczewski, K., Ong, Y.T., Li, Z., Griffin, D.T., Schuckmann, M.M., Tanuma, J., Oka, S., Singh, K., Kodama, E.N., Sarafianos, S.G.

(2012) J Biol Chem 287: 29988-29999

PubMed: 22761416 Search on PubMedSearch on PubMed Central
DOI: 10.1074/jbc.M112.351551
Primary Citation of Related Structures:
4DG1

PubMed Abstract:

Polymorphisms have poorly understood effects on drug susceptibility and may affect the outcome of HIV treatment. We have discovered that an HIV-1 reverse transcriptase (RT) polymorphism (RT(172K)) is present in clinical samples and in widely used laboratory strains (BH10), and it profoundly affects HIV-1 susceptibility to both nucleoside (NRTIs) and non-nucleoside RT inhibitors (NNRTIs) when combined with certain mutations. Polymorphism 172K significantly suppressed zidovudine resistance caused by excision (e.g. thymidine-associated mutations) and not by discrimination mechanism mutations (e.g. Q151M complex). Moreover, it attenuated resistance to nevirapine or efavirenz imparted by NNRTI mutations. Although 172K favored RT-DNA binding at an excisable pre-translocation conformation, it decreased excision by thymidine-associated mutation-containing RT. 172K affected DNA handling and decreased RT processivity without significantly affecting the k(cat)/K(m) values for dNTP. Surface plasmon resonance experiments revealed that RT(172K) decreased DNA binding by increasing the dissociation rate. Hence, the increased zidovudine susceptibility of RT(172K) results from its increased dissociation from the chain-terminated DNA and reduced primer unblocking. We solved a high resolution (2.15 Å) crystal structure of RT mutated at 172 and compared crystal structures of RT(172R) and RT(172K) bound to NNRTIs or DNA/dNTP. Our structural analyses highlight differences in the interactions between α-helix E (where 172 resides) and the active site β9-strand that involve the YMDD loop and the NNRTI binding pocket. Such changes may increase dissociation of DNA, thus suppressing excision-based NRTI resistance and also offset the effect of NNRTI resistance mutations thereby restoring NNRTI binding.

Organizational Affiliation:

Christopher S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse Transcriptase P66 subunit	A	549	Human immunodeficiency virus type 1 BH10	Mutation(s): 3 Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse Transcriptase P51 subunit	B	427	Human immunodeficiency virus type 1 BH10	Mutation(s): 1 Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain M [A] SDF format, chain W [B] SDF format, chain Y [B] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain M [A] MOL2 format, chain W [B] MOL2 format, chain Y [B]	A, B	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain P [A] SDF format, chain Q [A] SDF format, chain S [B] SDF format, chain T [B] SDF format, chain U [B] SDF format, chain V [B] SDF format, chain X [B] SDF format, chain Z [B] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain P [A] MOL2 format, chain Q [A] MOL2 format, chain S [B] MOL2 format, chain T [B] MOL2 format, chain U [B] MOL2 format, chain V [B] MOL2 format, chain X [B] MOL2 format, chain Z [B]	A, B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [A] SDF format, chain R [B] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain R [B]	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction