3QIO | pdb_00003qio

Crystal Structure of HIV-1 RNase H with engineered E. coli loop and N-hydroxy quinazolinedione inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3QIO/pdb

• Classification: TRANSFERASE, HYDROLASE/INHIBITOR
• Organism(s): HIV-1 M:B_HXB2R, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-27 Released: 2011-04-20 
• Deposition Author(s): Lansdon, E.B., Liu, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.

Lansdon, E.B., Liu, Q., Leavitt, S.A., Balakrishnan, M., Perry, J.K., Lancaster-Moyer, C., Kutty, N., Liu, X., Squires, N.H., Watkins, W.J., Kirschberg, T.A.

(2011) Antimicrob Agents Chemother 55: 2905-2915

• PubMed: 21464257 
• DOI: https://doi.org/10.1128/AAC.01594-10
• Primary Citation Related Structures: 
  3QIN, 3QIO, 3QIP


• PubMed Abstract: 
  

  HIV-1 RNase H breaks down the intermediate RNA-DNA hybrids during reverse transcription, requiring two divalent metal ions for activity. Pyrimidinol carboxylic acid and N-hydroxy quinazolinedione inhibitors were designed to coordinate the two metal ions in the active site of RNase H. High-resolution (1.4 Å to 2.1 Å) crystal structures were determined with the isolated RNase H domain and reverse transcriptase (RT), which permit accurate assessment of the metal and water environment at the active site. The geometry of the metal coordination suggests that the inhibitors mimic a substrate state prior to phosphodiester catalysis. Surface plasmon resonance studies confirm metal-dependent binding to RNase H and demonstrate that the inhibitors do not bind at the polymerase active site of RT. Additional evaluation of the RNase H site reveals an open protein surface with few additional interactions to optimize active-site inhibitors.

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Organizational Affiliation: 
• Gilead Sciences, Inc., 333 Lakeside Dr., Foster City, CA 94404, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 17.45 kDa 
• Atom Count: 1,292 
• Modeled Residue Count: 136 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein,Ribonuclease HI,Gag-Pol polyprotein	A	150	HIV-1 M:B_HXB2R, Escherichia coli K-12	Mutation(s): 0  Gene Names: gag-pol, rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4  Go to UniProtKB:  P0A7Y4
UniProt Groups	P04585P0A7Y4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QID	E [auth A]	3-hydroxy-6-(phenylsulfonyl)quinazoline-2,4(1H,3H)-dione C14 H10 N2 O5 S OWPKYKLZQGFBAE-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.905	α = 90
b = 56.352	β = 90
c = 64.038	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Lansdon, E.B., Liu, Q.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-07
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description