Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.50 kDa 
• Atom Count: 2043 
• Residue Count: 260 
• Unique protein chains: 1

1ES3

C98A mutant of streptomyces K15 DD-transpeptidase

• DOI: 10.2210/pdb1ES3/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. K15
• Expression System: Streptomyces lividans TK24
• Mutation(s): Yes 


• Deposited: 2000-04-07 Released: 2000-05-03 
• Deposition Author(s): Fonze, E., Charlier, P.

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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 

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

• PubMed: 12627955 
• DOI: 10.1021/bi027256x
• Structures With Same Primary Citation


• 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 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DD-TRANSPEPTIDASE	A	262	Streptomyces sp. K15	Mutation(s): 1  EC: 3.4.16.4
Find proteins for P39042 (Streptomyces sp. (strain K15)) Explore P39042  Go to UniProtKB:  P39042

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 46.305	α = 90
b = 54.09	β = 90
c = 108.769	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
SAINT	data reduction
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-07 
• Released Date: 2000-05-03 
Deposition Author(s): Fonze, E., Charlier, P.

Revision History 

• 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