5ZQB

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Penicillin G bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity

Jeong, J.H.Cha, H.J.Kim, Y.G.

(2018) Antimicrob Agents Chemother 62

  • DOI: https://doi.org/10.1128/AAC.00796-18
  • Primary Citation of Related Structures:  
    5ZQA, 5ZQB, 5ZQC, 5ZQD, 5ZQE

  • PubMed Abstract: 

    β-Lactam antibiotics that inhibit penicillin-binding proteins (PBPs) have been widely used in the treatment of bacterial infections. However, the molecular basis underlying the different inhibitory potencies of β-lactams against specific PBPs is not fully understood. Here, we present the crystal structures of penicillin-binding protein D2 (PBPD2) from Listeria monocytogenes , a Gram-positive foodborne bacterial pathogen that causes listeriosis in humans. The acylated structures in complex with four antibiotics (penicillin G, ampicillin, cefotaxime, and cefuroxime) revealed that the β-lactam core structures were recognized by a common set of residues; however, the R1 side chains of each antibiotic participate in different interactions with PBPD2. In addition, the structural complementarities between the side chains of β-lactams and the enzyme were found to be highly correlated with the relative reactivities of penam or cephem antibiotics against PBPD2. Our study provides the structural basis for the inhibition of PBPD2 by clinically important β-lactam antibiotics that are commonly used in listeriosis treatment. Our findings imply that the modification of β-lactam side chains based on structural complementarity could be useful for the development of potent inhibitors against β-lactam-resistant PBPs.


  • Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lmo2812 protein
A, B, C, D
276Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: lmo2812
UniProt
Find proteins for Q8Y3M3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y3M3 
Go to UniProtKB:  Q8Y3M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y3M3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNM (Subject of Investigation/LOI)
Query on PNM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
M [auth D]
OPEN FORM - PENICILLIN G
C16 H20 N2 O4 S
OGFZUTGOGYUTKZ-KWCYVHTRSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.716α = 90
b = 98.9β = 104.3
c = 77.453γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary