4PQA

Crystal Structure of succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58 in complex with the Inhibitor Captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.

Starus, A.Nocek, B.Bennett, B.Larrabee, J.A.Shaw, D.L.Sae-Lee, W.Russo, M.T.Gillner, D.M.Makowska-Grzyska, M.Joachimiak, A.Holz, R.C.

(2015) Biochemistry 54: 4834-4844

  • DOI: 10.1021/acs.biochem.5b00475
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding of the competitive inhibitor L-captopril to the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. L-Captopril, an angiotens ...

    Binding of the competitive inhibitor L-captopril to the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. L-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 μM and a measured Ki of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. L-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 μM. To examine the nature of the interaction of L-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with L-captopril at 1.8 Å resolution. Combination of these data provides new insights into binding of L-captopril to the active site of DapE enzymes as well as important inhibitor-active site residue interaction's. Such information is critical for the design of new, potent inhibitors of DapE enzymes.


    Organizational Affiliation

    ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States.,‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States.,#Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States.,†Department of Chemistry and Biochemistry, Loyola University-Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States.,⊥Department of Chemistry, Silesian University of Technology, 44-100 Gliwice, Poland.,§Department of Physics, Marquette University, Milwaukee, Wisconsin 53201, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-diaminopimelate desuccinylase
A
381Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Gene Names: dapE
EC: 3.5.1.18
Find proteins for Q9JYL2 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9JYL2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
X8Z
Query on X8Z

Download SDF File 
Download CCD File 
A
L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 116.921α = 90.00
b = 151.487β = 90.00
c = 55.098γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
HKL-3000data scaling
CCP4phasing
HKL-3000data reduction
CCP4model building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references