7LUU | pdb_00007luu

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.170 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.141 (Depositor) 
  • R-Value Observed: 
    0.143 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

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 Related Structures: 
    7LUU

  • 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.

Macromolecule Content 

  • Total Structure Weight: 34.8 kDa 
  • Atom Count: 2,472 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 307 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Subclass B3 metallo-beta-lactamase307Sphingobium indicum B90AMutation(s): 0 
Gene Names: SIDU_11385
UniProt
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.170 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.141 (Depositor) 
  • R-Value Observed: 0.143 (Depositor) 
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
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-11-06
    Changes: Structure summary