Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.19 kDa 
• Atom Count: 3173 
• Modelled Residue Count: 345 
• Deposited Residue Count: 349 
• Unique protein chains: 1

1PW1

Non-Covalent Complex Of Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin

• DOI: 10.2210/pdb1PW1/pdb

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


• Deposited: 2003-06-30 Released: 2004-07-13 
• Deposition Author(s): Silvaggi, N.R., Josephine, H.R., Pratt, R.F., Kelly, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.151 
• R-Value Work: 0.116 
• R-Value Observed: 0.116 

Literature

Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin"

Silvaggi, N.R., Josephine, H.R., Kuzin, A.P., Nagarajan, R., Pratt, R.F., Kelly, J.A.

(2005) J Mol Biol 345: 521-533

• PubMed: 15581896 
• DOI: 10.1016/j.jmb.2004.10.076
• Primary Citation of Related Structures:  
  1PW1, 1PW8, 1PWC, 1PWD, 1PWG


• PubMed Abstract: 
  

The bacterial D-alanyl-D-alanine transpeptidases (DD-peptidases) are the killing targets of beta-lactams, the most important clinical defense against bacterial infections. However, due to the constant development of antibiotic-resistance mechanisms by bacteria, there is an ever-present need for new, more effective antimicrobial drugs. While enormous numbers of beta-lactam compounds have been tested for antibiotic activity in over 50 years of research, the success of a beta-lactam structure in terms of antibiotic activity remains unpredictable. Tipper and Strominger suggested long ago that beta-lactams inhibit DD-peptidases because they mimic the D-alanyl-D-alanine motif of the peptidoglycan substrate of these enzymes. They also predicted that beta-lactams having a peptidoglycan-mimetic side-chain might be better antibiotics than their non-specific counterparts, but decades of research have not provided any evidence for this. We have recently described two such novel beta-lactams. The first is a penicillin having the glycyl-L-alpha-amino-epsilon-pimelyl side-chain of Streptomyces strain R61 peptidoglycan, making it the "perfect penicillin" for this organism. The other is a cephalosporin with the same side-chain. Here, we describe the X-ray crystal structures of the perfect penicillin in non-covalent and covalent complexes with the Streptomyces R61 DD-peptidase. The structure of the non-covalent enzyme-inhibitor complex is the first such complex to be trapped crystallographically with a DD-peptidase. In addition, the covalent complex of the peptidyl-cephalosporin with the R61 DD-peptidase is described. Finally, two covalent complexes with the traditional beta-lactams benzylpenicillin and cephalosporin C were determined for comparison with the peptidyl beta-lactams. These structures, together with relevant kinetics data, support Tipper and Strominger's assertion that peptidoglycan-mimetic side-chains should improve beta-lactams as inhibitors of DD-peptidases.

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Related Citations: 

• Structures of Two Kinetic Intermediates Reveal Species Specificity of Penicillin-Binding Proteins
  Mcdonough, M.A., Anderson, J.W., Silvaggi, N.R., Pratt, R.F., Knox, J.R., Kelly, J.A.
  (2002) J Mol Biol 322: 111

• A 1.2-A Snapshot of the Final Step of Bacterial Cell Wall Biosynthesis
  Lee, W., Mcdonough, M.A., Kotra, L., Li, Z.H., Silvaggi, N.R., Takeda, Y., Kelly, J.A., Mobashery, S.
  (2001) Proc Natl Acad Sci U S A 98: 1427

• The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution
  Kelly, J.A., Kuzin, A.P.
  (1995) J Mol Biol 254: 223

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Organizational Affiliation: 

Department of Molecular and Cell Biology and Institute for Materials Science, University of Connecticut, Storrs, CT 06269-3125, USA.

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEL (Subject of Investigation/LOI)	B [auth A]	(2S,5R,6R)-6-{[(6R)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLATE C17 H25 N4 O7 S LDJWRKFRKCXUDO-RBQWDTSBSA-M
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FOR	F [auth A], G [auth A]	FORMYL GROUP C H2 O WSFSSNUMVMOOMR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.151 
• R-Value Work: 0.116 
• R-Value Observed: 0.116 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51	α = 90
b = 67	β = 90
c = 100.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-30 
• Released Date: 2004-07-13 
Deposition Author(s): Silvaggi, N.R., Josephine, H.R., Pratt, R.F., Kelly, J.A.

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description