Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.53 kDa 
• Atom Count: 3210 
• Residue Count: 206 
• Unique protein chains: 2

4EQJ

Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate RT-RH

• DOI: 10.2210/pdb4EQJ/pdb

• Classification: hydrolase/hydrolase substrate
• Organism(s): HIV-1 M:B_ARV2/SF2, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-04-19 Released: 2012-06-06 
• Deposition Author(s): Schiffer, C.A., Mittal, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.

Alvizo, O., Mittal, S., Mayo, S.L., Schiffer, C.A.

(2012) Protein Sci 21: 1029-1041

• PubMed: 22549928 
• DOI: 10.1002/pro.2086
• Primary Citation of Related Structures:  
  4EP2, 4EP3, 4EQ0, 4EPJ, 4EQJ


• PubMed Abstract: 
  

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.

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Organizational Affiliation: 

Division of Biology, Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California 91125, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease, tethered dimer	A	203	HIV-1 M:B_ARV2/SF2	Mutation(s): 8  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
substrate RT-RH	G	8	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol EC: 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q9YV20 (Human immunodeficiency virus 1) Explore Q9YV20  Go to UniProtKB:  Q9YV20

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.994	α = 90
b = 59.286	β = 90
c = 62.13	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-19 
• Released Date: 2012-06-06 
Deposition Author(s): Schiffer, C.A., Mittal, S.

Revision History 

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Derived calculations
• Version 1.2: 2013-01-09
  Changes: Database references
• Version 1.3: 2017-07-26
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 1.4: 2017-11-15
  Changes: Refinement description