1D6S

CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYLASE COMPLEXED IN EXTERNAL ALDIMINE LINKAGE WITH METHIONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand binding induces a large conformational change in O-acetylserine sulfhydrylase from Salmonella typhimurium.

Burkhard, P.Tai, C.H.Ristroph, C.M.Cook, P.F.Jansonius, J.N.

(1999) J.Mol.Biol. 291: 941-953

  • DOI: 10.1006/jmbi.1999.3002

  • PubMed Abstract: 
  • Covalent binding of L-methionine as an external aldimine to the pyridoxal 5'-phosphate-cofactor in the K41A mutant of O-acetylserine sulfhydrylase from Salmonella typhimurium induces a large conformational change in the protein. Methionine mimics the ...

    Covalent binding of L-methionine as an external aldimine to the pyridoxal 5'-phosphate-cofactor in the K41A mutant of O-acetylserine sulfhydrylase from Salmonella typhimurium induces a large conformational change in the protein. Methionine mimics the action of the substrate O-acetyl-L-serine during catalysis. The alpha-carboxylate moiety of L-methionine in external aldimine linkage with the active site pyridoxal 5'-phosphate forms a hydrogen bonding network to the "asparagine-loop" P67-T68-N69-G70 which adopts a different conformation than in the native protein. The side-chain nitrogen of Asn69 moves more than 7 A to make a hydrogen bond to the alpha-carboxylate group of the inhibitor. As the external aldimine is formed, the PLP tilts by 13 degrees along its longitudinal axis such that C4' moves toward the entrance to the active site and the side-chain of the methionine is directed toward the active site entrance. The local rearrangement acts as a trigger to induce a large global conformational change in the protein. A subdomain comprised of beta-strand 4, alpha-helix 3, beta-strand 5 and alpha-helix 4 moves towards the active site by a rotation of 7 degrees. This subdomain movement results in a reduction of the severe twist of its central beta-sheet and reduces the active site entrance to a small hole, giving access only to small molecules like sulfide, the second substrate, or acetate, the first product.


    Related Citations: 
    • Three-dimensional Structure of O-Acetylserine Sulfhydrylase from Salmonella typhimurium
      Burkhard, P.,Rao, G.S.,Hohenester, E.,Schnackerz, K.D.,Cook, P.F.,Jansonius, J.N.
      (1998) J.Mol.Biol. 283: 121


    Organizational Affiliation

    Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, CH-4056, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-ACETYLSERINE SULFHYDRYLASE
A, B
322Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: cysK
EC: 2.5.1.47
Find proteins for P0A1E3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A1E3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A, B
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PLPKd: 78000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.940α = 90.00
b = 149.930β = 90.00
c = 53.640γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
CCP4data scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance