Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114632.33 
• Atom Count: 7968 
• Residue Count: 976 
• Unique protein chains: 2

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 group M subtype B (isolate BH10)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 4 


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

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Experimental Data Snapshot

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

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 
• DOI: 10.1074/jbc.M112.351551


• 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.

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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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Reverse Transcriptase P66 subunit	A	549	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)	Mutation(s): 3  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Reverse Transcriptase P51 subunit	B	427	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.247 
• R-Value Work: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 159.230	α = 90.00
b = 72.150	β = 97.52
c = 109.240	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2012-06-20
  Type: Initial release
• Version 1.1: 2012-07-25
  Type: Database references
• Version 1.2: 2012-09-12
  Type: Database references