4PQA | pdb_00004pqa

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

• PDB DOI: https://doi.org/10.2210/pdb4PQA/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli
• Mutation(s): No 


• 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 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

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: https://doi.org/10.1021/acs.biochem.5b00475
• Primary Citation Related Structures: 
  4O23, 4PPZ, 4PQA


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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 41.82 kDa 
• Atom Count: 3,242 
• Modeled Residue Count: 375 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A	381	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: dapE, NMB1530 EC: 3.5.1.18
UniProt
Find proteins for Q9JYL2 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9JYL2  Go to UniProtKB:  Q9JYL2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8Z	B [auth A]	L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.196 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34pqa

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.921	α = 90
b = 151.487	β = 90
c = 55.098	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations