4H2K

Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The dimerization domain in DapE enzymes is required for catalysis.

Nocek, B.Starus, A.Makowska-Grzyska, M.Gutierrez, B.Sanchez, S.Jedrzejczak, R.Mack, J.C.Olsen, K.W.Joachimiak, A.Holz, R.C.

(2014) Plos One 9: e93593-e93593

  • DOI: 10.1371/journal.pone.0093593
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial pept ...

    The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role of each domain of the enzyme we engineered dimerization domain deletion mutants of DapEs from Haemophilus influenzae and Vibrio cholerae, and characterized these proteins structurally and biochemically. No activity was observed for all deletion mutants. Structural comparisons of wild-type, inactive monomeric DapE enzymes with other M20 peptidases suggest that the dimerization domain is essential for DapE enzymatic activity. Structural analysis and molecular dynamics simulations indicate that removal of the dimerization domain increased the flexibility of a conserved active site loop that may provide critical interactions with the substrate.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-diaminopimelate desuccinylase
A, B
269Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: dapE
EC: 3.5.1.18
Find proteins for P44514 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44514
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 61.667α = 90.00
b = 44.721β = 92.90
c = 92.481γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy