1YQS

Inhibition of the R61 DD-Peptidase by N-benzoyl-beta-sultam

• PDB DOI: https://doi.org/10.2210/pdb1YQS/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp. R61
• Mutation(s): No 


• Deposited: 2005-02-02 Released: 2005-06-28 
• Deposition Author(s): Ahmed, N., Cordaro, M., Laws, A.P., Delmarcelle, M., Silvaggi, N.R., Kelly, J.A., Page, M.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.136 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 

Literature

Inactivation of Bacterial dd-Peptidase by beta-Sultams.

Ahmed, N., Cordaro, M., Laws, A.P., Delmarcelle, M., Silvaggi, N.R., Kelly, J.A., Page, M.I.

(2005) Biochemistry 44: 7738-7746

• PubMed: 15909988 
• DOI: https://doi.org/10.1021/bi050110o
• Primary Citation of Related Structures:  
  1YQS


• PubMed Abstract: 
  

  N-Acyl-beta-sultams are time-dependent, irreversible active site-directed inhibitors of Streptomyces R61 DD-peptidase. The rate of inactivation is first order with respect to beta-sultam concentration, and the second-order rate constants show a dependence on pH similar to that for the hydrolysis of a substrate. Inactivation is due to the formation of a stable 1:1 enzyme-inhibitor complex as a result of the active site serine being sulfonylated by the beta-sultam as shown by ESI-MS analysis and by X-ray crystallography. A striking feature of the sulfonyl enzyme is that the inhibitor is not bound to the oxyanion hole but interacts extensively with the "roof" of the active site where the Arg 285 is located.

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Organizational Affiliation: 

Department of Chemical and Biological Sciences, The University of Huddersfield, Huddersfield HD1 3DH, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.07 kDa 
• Atom Count: 3,095 
• Modelled Residue Count: 345 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase	A	349	Streptomyces sp. R61	Mutation(s): 0  EC: 3.4.16.4
UniProt
Find proteins for P15555 (Streptomyces sp. (strain R61)) Explore P15555  Go to UniProtKB:  P15555

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BSA	B [auth A], C [auth A]	2-(BENZOYLAMINO)ETHANESULFONIC ACID C9 H11 N O4 S ABUKAMCDAHVPSR-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.136 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.8	α = 90
b = 66.7	β = 90
c = 100.5	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Ahmed, N., Cordaro, M., Laws, A.P., Delmarcelle, M., Silvaggi, N.R., Kelly, J.A., Page, M.I.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description