1ES3

C98A mutant of streptomyces K15 DD-transpeptidase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.

Rhazi, N., Charlier, P., Dehareng, D., Engher, D., Vermeire, M., Frere, J.M., Nguyen-Disteche, M., Fonze, E.

(2003) Biochemistry 42: 2895-2906

  • DOI: 10.1021/bi027256x
  • Primary Citation of Related Structures:  
    1ES2, 1ES3, 1ES4, 1J9M

  • PubMed Abstract: 

    • The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis ...

    The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis. The Lys38His and Ser96Ala mutations almost completely abolished the penicillin binding and severely impaired the transpeptidase activities while the geometry of the active site was essentially the same as in the wild-type enzyme. It is proposed that Lys38 acts as the catalytic base that abstracts a proton from the active serine Ser35 during nucleophilic attack and that Ser96 is a key intermediate in the proton transfer from the Ogamma of Ser35 to the substrate leaving group nitrogen. The role of these two residues should be conserved among penicillin-binding proteins containing the Ser-Xaa-Asn/Cys sequence in motif 2. Conversion of Cys98 into Asn decreased the transpeptidase activity and increased hydrolysis of the thiolester substrate and the acylation rate with most beta-lactam antibiotics. Cys98 is proposed to play the same role as Asn in motif 2 of other penicilloyl serine transferases in properly positioning the substrate for the catalytic process.

    Related Citations: 
    • The Crystal Structure of a Penicilloyl-Serine Transferase of Intermediate Penicillin Sensitivity
      Fonze, E., Vermeire, M., Nguyen-Disteche, M., Brasseur, R., Charlier, P.
      (1999) J Biol Chem 274: 21853
    • Crystallization and X-Ray Diffraction Study of the Streptomyces K15 Penicillin-Binding Dd-Transpeptidase
      Englebert, S., Charlier, P., Fonze, E., To'Th, Y., Vermeire, M., Van Beeumen, J., Grandchamps, J., Hoffmann, K., Leyh-Bouille, M., Nguyen-Disteche, M., Ghuysen, J.-M.
      (1994) J Mol Biol 241: 295
    Organizational Affiliation: 

    Institut de Physique B5 and Institut de Chimie B6, Centre d'Ingénierie des Protéines, Université de Liège, B-4000 Sart Tilman, Belgium.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DD-TRANSPEPTIDASEA262Streptomyces sp. K15Mutation(s): 1 
EC: 3.4.16.4
UniProt
Find proteins for P39042 (Streptomyces sp. (strain K15))
Explore P39042 
Go to UniProtKB:  P39042
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39042
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.305α = 90
b = 54.09β = 90
c = 108.769γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
AMoREphasing
X-PLORrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations