3T4P

Crystal structure of O-Acetyl Serine Sulfhydrylase from Leishmania donovani in complex with designed tetrapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences

Raj, I.Kumar, S.Gourinath, S.

(2012) Acta Crystallogr.,Sect.D 68: 909-919

  • DOI: 10.1107/S0907444912016459
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cysteine is a crucial substrate for the synthesis of glutathione and trypanothione, which in turn maintain intracellular redox homeostasis and defend against oxidative stress in the pathogen Leishmania donovani. Here, the identification, sequencing, ...

    Cysteine is a crucial substrate for the synthesis of glutathione and trypanothione, which in turn maintain intracellular redox homeostasis and defend against oxidative stress in the pathogen Leishmania donovani. Here, the identification, sequencing, characterization and crystal structure at 1.79 Å resolution of O-acetylserine sulfhydrylase (OASS), a cysteine-biosynthetic pathway enzyme from L. donovani (LdOASS), are reported. It shows binding to the serine acetyltransferase (SAT) C-terminal peptide, indicating that OASS and SAT interact with each other to form a cysteine synthase complex, further confirmed by the structure of LdOASS in complex with SAT C-terminal octapeptide at 1.68 Å resolution. Docking and fluorescence binding studies show that almost all SAT C-terminus mimicking tetrapeptides can bind to LdOASS. Some peptides had a higher binding affinity than the native peptide, indicating that SAT-OASS interactions are not sequence-specific. The structure of LdOASS with a designed peptide (DWSI) revealed that LdOASS makes more interactions with the designed peptide than with the native peptide. In almost all known SAT-OASS interactions the SAT C-terminal sequence was shown to contain amino acids with large side chains. Structural comparison with other OASSs revealed that LdOASS has a relatively less open active-site cleft, which may be responsible for its interaction with the smaller-amino-acid-containing C-terminal LdSAT peptide. Biochemical studies confirmed that LdOASS interacts with SATs from Entamoeba histolytica and Brucella abortus, further displaying its sequence-independent and versatile mode of interaction with SATs. This implicates a critical role of the size of the active-site cleft opening in OASS for SAT-OASS interaction and thus cysteine synthase complex formation.


    Organizational Affiliation

    School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-acetyl serine sulfhydrylase
A
334Leishmania donovaniMutation(s): 0 
Gene Names: OASS
Find proteins for G1C2I2 (Leishmania donovani)
Go to UniProtKB:  G1C2I2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tetrapeptide DWSI
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 115.300α = 90.00
b = 61.930β = 90.00
c = 43.440γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data collection
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-26 
  • Released Date: 2012-08-01 
  • Deposition Author(s): Raj, I., Gourinath, S.

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description