Crystallographic structure of DapE from Enterococcus faecium

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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The three-dimensional structure of DapE from Enterococcus faecium reveals new insights into DapE/ArgE subfamily ligand specificity.

Terrazas-Lopez, M.Gonzalez-Segura, L.Diaz-Vilchis, A.Aguirre-Mendez, K.A.Lobo-Galo, N.Martinez-Martinez, A.Diaz-Sanchez, A.G.

(2024) Int J Biol Macromol 270: 132281-132281

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.132281
  • Primary Citation of Related Structures:  
    7UOI, 8VKT

  • PubMed Abstract: 

    DapE is a Zn 2+ -metallohydrolase recognized as a drug target for bacterial control. It is a homodimer that requires the exchange of interface strands by an induced fit essential for catalysis. Identifying novel anti-DapE agents requires greater structural details. Most of the characterized DapEs are from the Gram-negative group. Here, two high-resolution DapE crystal structures from Enterococcus faecium are presented for the first time with novel aspects. A loosened enzyme intermediate between the open and closed conformations is observed. Substrates may bind to loose state, subsequently it closes, where hydrolysis occurs, and finally, the change to the open state leads to the release of the products. Mutation of His352 suggests a role, along with His194, in the oxyanion stabilization in the mono-metalated Zn 2+ isoform, while in the di-metalated isoform, the metal center 2 complements it function. An aromatic-π box potentially involved in the interaction of DapE with other proteins, and a peptide flip could determine the specificity in the Gram-positive ArgE/DapE group. Finally, details of two extra-catalytic cavities whose geometry changes depending on the conformational state of the enzyme are presented. These cavities could be a target for developing non-competitive agents that trap the enzyme in an inactive state.

  • Organizational Affiliation

    Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
succinyl-diaminopimelate desuccinylase402Enterococcus faecium 1,231,410Mutation(s): 0 
Gene Names: EFTG_01132
Find proteins for A0A1S8KJG1 (Enterococcus faecium)
Explore A0A1S8KJG1 
Go to UniProtKB:  A0A1S8KJG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S8KJG1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.486α = 90
b = 45.378β = 103.65
c = 78.751γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoPN-2015-587
Facultad de QuimicaMexicoUNAM 5000-9129
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)MexicoIN227920

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Author supporting evidence
  • Version 1.2: 2024-05-22
    Changes: Data collection
  • Version 1.3: 2024-06-12
    Changes: Database references