Kinetic and Structural Characterization of the First B3 Metallo-beta-Lactamase with an Active Site Glutamic Acid

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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Kinetic and Structural Characterization of the First B3 Metallo-beta-Lactamase with an Active-Site Glutamic Acid.

Wilson, L.A.Knaven, E.G.Morris, M.T.Monteiro Pedroso, M.Schofield, C.J.Bruck, T.B.Boden, M.Waite, D.W.Hugenholtz, P.Guddat, L.Schenk, G.

(2021) Antimicrob Agents Chemother 65: e0093621-e0093621

  • DOI: https://doi.org/10.1128/AAC.00936-21
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active-site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations, were reported previously. Here, we describe the structure and kinetic properties of the first example (SIE-1) of a fourth variant containing the EHH/DHH active-site motif (B3-E). SIE-1 was identified in the hexachlorocyclohexane-degrading bacterium Sphingobium indicum, and kinetic analyses demonstrate that although it is active against a wide range of antibiotics, its efficiency is lower than that of other B3 MBLs but has increased efficiency toward cephalosporins relative to other β-lactam substrates. The overall fold of SIE-1 is characteristic of the MBLs; the notable variation is observed in the Zn1 site due to the replacement of the canonical His116 by a glutamate. The unusual preference of SIE-1 for cephalosporins and its occurrence in a widespread environmental organism suggest the scope for increased MBL-mediated β-lactam resistance. Thus, it is relevant to include SIE-1 in MBL inhibitor design studies to widen the therapeutic scope of much needed antiresistance drugs.

  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, The University of Queenslandgrid.1003.2, St. Lucia, QLD, Brisbane, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subclass B3 metallo-beta-lactamase307Sphingobium indicum B90AMutation(s): 0 
Gene Names: SIDU_11385
Find proteins for A0A1L5BQA7 (Sphingobium indicum (strain DSM 16412 / CCM 7286 / MTCC 6364 / B90A))
Explore A0A1L5BQA7 
Go to UniProtKB:  A0A1L5BQA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L5BQA7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A],
D [auth A],
E [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C3 H8 O3
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.64α = 90
b = 75.42β = 90
c = 56.67γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1084778

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description