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 
  • R-Value Observed: 0.164 

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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:  
    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 ...

    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, Marquette University, Milwaukee, Wisconsin 53201, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-diaminopimelate desuccinylaseA381Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: dapE, NMB1530
EC: 3.5.1.18
UniProt
Find proteins for Q9JYL2 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JYL2 
Go to UniProtKB:  Q9JYL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JYL2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X8Z
Query on X8Z
Download Ideal Coordinates CCD File 
B [auth A]L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.921α = 90
b = 151.487β = 90
c = 55.098γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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