2V03

High resolution structure and catalysis of an O-acetylserine sulfhydrylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High resolution structure and catalysis of O-acetylserine sulfhydrylase isozyme B from Escherichia coli.

Zocher, G.Wiesand, U.Schulz, G.E.

(2007) FEBS J 274: 5382-5389

  • DOI: 10.1111/j.1742-4658.2007.06063.x
  • Primary Citation of Related Structures:  
    2V03

  • PubMed Abstract: 
  • The crystal structure of the dimeric O-acetylserine sulfhydrylase isozyme B from Escherichia coli (CysM), complexed with the substrate analog citrate, has been determined at 1.33 A resolution by X-ray diffraction analysis. The C1-carboxylate of citra ...

    The crystal structure of the dimeric O-acetylserine sulfhydrylase isozyme B from Escherichia coli (CysM), complexed with the substrate analog citrate, has been determined at 1.33 A resolution by X-ray diffraction analysis. The C1-carboxylate of citrate was bound at the carboxylate position of O-acetylserine, whereas the C6-carboxylate adopted two conformations. The activity of the enzyme and of several active center mutants was determined using an assay based on O-acetylserine and thio-nitrobenzoate (TNB). The unnatural substrate TNB was modeled into the reported structure. The substrate model and the observed mutant activities may facilitate future protein engineering attempts designed to broaden the substrate spectrum of the enzyme. A comparison of the reported structure with previously published CysM structures revealed large conformational changes. One of the crystal forms contained two dimers, each of which comprised one subunit in a closed and one in an open conformation. Although the homodimer asymmetry was most probably caused by crystal packing, it indicates that the enzyme can adopt such a state in solution, which may be relevant for the catalytic reaction.


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine synthase BA303Escherichia coli K-12Mutation(s): 1 
Gene Names: cysMb2421JW2414
EC: 2.5.1.47
Find proteins for P16703 (Escherichia coli (strain K12))
Explore P16703 
Go to UniProtKB:  P16703
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.615α = 90
b = 76.615β = 90
c = 209.787γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2015-11-11
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 1.3: 2018-07-25
    Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary