1MB9 | pdb_00001mb9

BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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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: 110.84 kDa 
  • Atom Count: 7,960 
  • Modeled Residue Count: 982 
  • 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
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Reference Sequence

Small Molecules

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

Query on ATP



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
AMP

Query on AMP



Download:Ideal Coordinates CCD File
F [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
POP

Query on POP



Download:Ideal Coordinates CCD File
E [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
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: 2.11 Å
  • R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.252α = 90
b = 97.571β = 90.69
c = 81.313γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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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: 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