1MBZ | pdb_00001mbz

BETA-LACTAM SYNTHETASE WITH TRAPPED INTERMEDIATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1MBZ

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots

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

(2002) Proc Natl Acad Sci U S A 99: 14752-14757

  • DOI: https://doi.org/10.1073/pnas.232361199
  • Primary Citation Related Structures: 
    1M1Z, 1MB9, 1MBZ, 1MC1

  • PubMed Abstract: 

    The catalytic cycle of the ATP/Mg(2+)-dependent enzyme beta-lactam synthetase (beta-LS) from Streptomyces clavuligerus has been observed through a series of x-ray crystallographic snapshots. Chemistry is initiated by the ordered binding of ATP/Mg(2+) and N(2)-(carboxyethyl)-l-arginine (CEA) to the apoenzyme. The apo and ATP/Mg(2+) structures described here, along with the previously described CEA.alpha,beta-methyleneadenosine 5'-triphosphate (CEA.AMP-CPP)/Mg(2+) structure, illuminate changes in active site geometry that favor adenylation. In addition, an acyladenylate intermediate has been trapped. The substrate analog N(2)-(carboxymethyl)-l-arginine (CMA) was adenylated by ATP in the crystal and represents a close structural analog of the previously proposed CEA-adenylate intermediate. Finally, the structure of the ternary product complex deoxyguanidinoproclavaminic acid (DGPC).AMP/PP(i)/Mg(2+) has been determined. The CMA-AMP/PP(i)/Mg(2+) and DGPC.AMP/PP(i)/Mg(2+) structures reveal interactions in the active site that facilitate beta-lactam formation. All of the ATP-bound structures differ from the previously described CEA.AMP-CPP/Mg(2+) structure in that two Mg(2+) ions are found in the active sites. These Mg(2+) ions play critical roles in both the adenylation and beta-lactamization reactions.


  • Organizational Affiliation
    • Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA.

Macromolecule Content 

  • Total Structure Weight: 110.96 kDa 
  • Atom Count: 7,918 
  • Modeled Residue Count: 990 
  • Deposited Residue Count: 1,026 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-LACTAM SYNTHETASE
A, B
513Streptomyces clavuligerusMutation(s): 0 
Gene Names: 1901
EC: 6.3.3.4
UniProt
Find proteins for P0DJQ7 (Streptomyces clavuligerus)
Explore P0DJQ7 
Go to UniProtKB:  P0DJQ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJQ7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOT

Query on IOT



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
ARGININE-N-METHYLCARBONYL PHOSPHORIC ACID 5'-ADENOSINE ESTER
C18 H28 N9 O10 P
PLEMKERVZBXYMR-CWPZRQPOSA-N
POP

Query on POP



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.39α = 90
b = 97.154β = 90.11
c = 81.087γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description