4O23

Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 

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, Loyola University-Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-diaminopimelate desuccinylase
A, B
384Neisseria 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 2 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
SO4
Query on SO4

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

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 55.324α = 90.00
b = 111.389β = 90.00
c = 132.535γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
MOLREPphasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references