5YQ8 | pdb_00005yq8

Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major

• PDB DOI: https://doi.org/10.2210/pdb5YQ8/pdb

• Classification: HYDROLASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-06 Released: 2018-09-19 
• Deposition Author(s): Suguna, K., Kumar, S.
• Funding Organization(s): Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.240 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein.

Kumar, S., Suguna, K.

(2018) FEBS Open Bio 8: 1379-1394

• PubMed: 30186740 
• DOI: https://doi.org/10.1002/2211-5463.12491
• Primary Citation Related Structures: 
  5YQ8, 5YS4


• PubMed Abstract: 
  

  DNA damage-inducible 1 (Ddi1) is a multidomain protein with one of the domains being retropepsin-like. HIV-1 protease inhibitors were found to reduce opportunistic infections caused by pathogens like Leishmania and Plasmodium , and some of them were shown to inhibit the growth of these parasites. In Leishmania , Ddi1 was identified as a likely target of the inhibitors. We report the crystal structure of the retropepsin-like domain of Ddi1 from Leishmania major as a dimer with clear density for the critical 'flap' region. We have characterized binding with one of the HIV-1 protease inhibitors in solution using bio-layer interferometry and by docking. Further, we have performed molecular dynamics (MD) simulation studies that show that the protein undergoes a conformational change from open to semi-open and closed forms with the closing of the flexible flap over the active site.

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Organizational Affiliation: 
• Molecular Biophysics Unit Indian Institute of Science Bangalore India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.24 kDa 
• Atom Count: 4,407 
• Modeled Residue Count: 510 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-damage inducible protein DDI1-like protein	A, B, C, D	130	Leishmania major	Mutation(s): 0  Gene Names: LMJF_01_0610 EC: 3.4.23
UniProt
Find proteins for I7HUG0 (Leishmania major) Explore I7HUG0  Go to UniProtKB:  I7HUG0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.240 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.53	α = 90
b = 80.39	β = 90
c = 85.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Suguna, K., Kumar, S.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering	India	--

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description