1JGT

CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine.

Miller, M.T.Bachmann, B.O.Townsend, C.A.Rosenzweig, A.C.

(2001) Nat.Struct.Mol.Biol. 8: 684-689

  • DOI: 10.1038/90394

  • PubMed Abstract: 
  • The enzyme beta-lactam synthetase (beta-LS) catalyzes the formation of the beta-lactam ring in clavulanic acid, a clinically important beta-lactamase inhibitor. Whereas the penicillin beta-lactam ring is generated by isopenicillin N synthase (IPNS) i ...

    The enzyme beta-lactam synthetase (beta-LS) catalyzes the formation of the beta-lactam ring in clavulanic acid, a clinically important beta-lactamase inhibitor. Whereas the penicillin beta-lactam ring is generated by isopenicillin N synthase (IPNS) in the presence of ferrous ion and dioxygen, beta-LS uses ATP and Mg2+ as cofactors. According to sequence alignments, beta-LS is homologous to class B asparagine synthetases (AS-Bs), ATP/Mg2+-dependent enzymes that convert aspartic acid to asparagine. Here we report the first crystal structure of a beta-LS. The 1.95 A resolution structure of Streptomyces clavuligerus beta-LS provides a fully resolved view of the active site in which substrate, closely related ATP analog alpha,beta-methyleneadenosine 5'-triphosphate (AMP-CPP) and a single Mg2+ ion are present. A high degree of substrate preorganization is observed. Comparison to Escherichia coli AS-B reveals the evolutionary changes that have taken place in beta-LS that impede interdomain reaction, which is essential in AS-B, and that accommodate beta-lactam formation. The structural data provide the opportunity to alter the synthetic potential of beta-LS, perhaps leading to the creation of new beta-lactamase inhibitors and beta-lactam antibiotics.


    Organizational Affiliation

    Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAM SYNTHETASE
A, B
513Streptomyces clavuligerusGene Names: bls
EC: 6.3.3.4
Find proteins for P0DJQ7 (Streptomyces clavuligerus)
Go to UniProtKB:  P0DJQ7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
APC
Query on APC

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A, B
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CMA
Query on CMA

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Download CCD File 
A, B
N2-(CARBOXYETHYL)-L-ARGININE
C9 H18 N4 O4
OHWCFZJEIHZWMN-LURJTMIESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.352α = 90.00
b = 97.873β = 90.78
c = 80.969γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
MAR345data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description