4ONW | pdb_00004onw

Crystal structure of the catalytic domain of DapE protein from V.cholerea

• PDB DOI: https://doi.org/10.2210/pdb4ONW/pdb
• Entry: 4ONW supersedes: 3T68

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-29 Released: 2014-04-23 
• Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Jedrzejczak, R., Gu, M., 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: 1.65 Å
• R-Value Free: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

The Dimerization Domain in DapE Enzymes Is required for Catalysis.

Nocek, B., Starus, A., Makowska-Grzyska, M., Gutierrez, B., Sanchez, S., Jedrzejczak, R., Mack, J.C., Olsen, K.W., Joachimiak, A., Holz, R.C.

(2014) PLoS One 9: e93593-e93593

• PubMed: 24806882 
• DOI: https://doi.org/10.1371/journal.pone.0093593
• Primary Citation Related Structures: 
  4H2K, 4ONW, 4OP4


• PubMed Abstract: 
  

  The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role of each domain of the enzyme we engineered dimerization domain deletion mutants of DapEs from Haemophilus influenzae and Vibrio cholerae, and characterized these proteins structurally and biochemically. No activity was observed for all deletion mutants. Structural comparisons of wild-type, inactive monomeric DapE enzymes with other M20 peptidases suggest that the dimerization domain is essential for DapE enzymatic activity. Structural analysis and molecular dynamics simulations indicate that removal of the dimerization domain increased the flexibility of a conserved active site loop that may provide critical interactions with the substrate.

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Organizational Affiliation: 
• Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
The Department of Chemistry and Biochemistry, Loyola University-Chicago, Chicago, Illinois, United States of America.
The Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America; The Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
Department of Chemistry, Marquette University, Milwaukee, Wisconsin, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.39 kDa 
• Atom Count: 4,697 
• Modeled Residue Count: 530 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A, B	268	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: dapE, VC_2152 EC: 3.5.1.18
UniProt
Find proteins for Q9KQ52 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ52  Go to UniProtKB:  Q9KQ52

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BU1	D [auth A], E [auth A], H [auth B], J [auth B], K [auth B], L [auth B]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34onw

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.649	α = 90
b = 49.649	β = 90
c = 232.566	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Jedrzejczak, R., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3T68

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2014-07-23
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description