3IQH

Structure of O-Acetylserine Sulfhydrylase in Complex with Peptide MNYDI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MNYDIB [auth P]5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth X]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.153α = 90
b = 112.153β = 90
c = 45.728γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2009-08-20 
  • Released Date: 2009-11-17 
  • Deposition Author(s): Roderick, S.L.

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