Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41817.78 
• Atom Count: 2898 
• Residue Count: 381 
• Unique protein chains: 1

4PQA

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

• DOI: 10.2210/pdb4PQA/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Neisseria meningitidis serogroup B (strain MC58)
• Expression System: Escherichia coli


• Deposited: 2014-03-01 Released: 2014-04-30 
• Deposition Author(s): Nocek, B., Starus, A., Holz, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

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

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

• PubMed: 26186504 
• DOI: 10.1021/acs.biochem.5b00475
• Primary Citation of Related Structures:  
  4PPZ, 4O23


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Succinyl-diaminopimelate desuccinylase	A	381	Neisseria 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
X8Z	A	L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.196 
• R-Value Work: 0.162 
• Space Group: C 2 2 2₁
• Diffraction Data DOI: 
  10.18430/M34PQA Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 116.921	α = 90.00
b = 151.487	β = 90.00
c = 55.098	γ = 90.00

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
HKL-3000	data scaling
CCP4	phasing
HKL-3000	data reduction
CCP4	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-03-01 
• Released Date: 2014-04-30 
• Deposition Author(s): Nocek, B., Starus, A., Holz, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History 

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