3IQI

Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNENI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of o-acetylserine sulfhydrylase inhibitors by mimicking nature.

Salsi, E.Bayden, A.S.Spyrakis, F.Amadasi, A.Campanini, B.Bettati, S.Dodatko, T.Cozzini, P.Kellogg, G.E.Cook, P.F.Roderick, S.L.Mozzarelli, A.

(2010) J Med Chem 53: 345-356

  • DOI: https://doi.org/10.1021/jm901325e
  • Primary Citation of Related Structures:  
    3IQG, 3IQH, 3IQI

  • PubMed Abstract: 

    The inhibition of cysteine biosynthesis in prokaryotes and protozoa has been proposed to be relevant for the development of antibiotics. Haemophilus influenzae O-acetylserine sulfhydrylase (OASS), catalyzing l-cysteine formation, is inhibited by the insertion of the C-terminal pentapeptide (MNLNI) of serine acetyltransferase into the active site. Four-hundred MNXXI pentapeptides were generated in silico, docked into OASS active site using GOLD, and scored with HINT. The terminal P5 Ile accounts for about 50% of the binding energy. Glu or Asp at position P4 and, to a lesser extent, at position P3 also significantly contribute to the binding interaction. The predicted affinity of 14 selected pentapeptides correlated well with the experimentally determined dissociation constants. The X-ray structure of three high affinity pentapeptide-OASS complexes were compared with the docked poses. These results, combined with a GRID analysis of the active site, allowed us to define a pharmacophoric scaffold for the design of peptidomimetic inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Parma, Italy. andrea.mozzarelli@unipr.it


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine synthaseA [auth X]316Haemophilus influenzaeMutation(s): 0 
Gene Names: cysKHI1103
EC: 2.5.1.47
UniProt
Find proteins for P45040 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P45040 
Go to UniProtKB:  P45040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45040
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MNENIB [auth P]5N/AMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A [auth X]L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.264α = 90
b = 112.264β = 90
c = 45.835γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection