6BDX

4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae

• PDB DOI: https://doi.org/10.2210/pdb6BDX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-24 Released: 2018-08-29 
• Deposition Author(s): Pote, S.S., Pye, S.E., Sheahan, T.E., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog.

Pote, S., Pye, S.E., Sheahan, T.E., Gawlicka-Chruszcz, A., Majorek, K.A., Chruszcz, M.

(2018) Biochem Biophys Res Commun 503: 1993-1999

• PubMed: 30093108 
• DOI: https://doi.org/10.1016/j.bbrc.2018.07.147
• Primary Citation of Related Structures:  
  6BDX


• PubMed Abstract: 
  

  Neisseria gonorrhoeae, an obligate human pathogen, is a leading cause of communicable diseases globally. Due to rapid development of drug resistance, the rate of successfully curing gonococcal infections is rapidly decreasing. Hence, research is being directed toward finding alternative drugs or drug targets to help eradicate these infections. 4-Hydroxy-tetrahydrodipicolinate reductase (DapB), an important enzyme in the meso-diaminopimelate pathway, is a promising target for the development of new antibiotics. This manuscript describes the first structure of DapB from N. gonorrhoeae determined at 1.85 Å. This enzyme uses NAD(P)H as cofactor. Details of the interactions of the enzyme with its cofactors and a substrate analog/inhibitor are discussed. A large scale bioinformatics analysis of DapBs' sequences is also described.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.13 kDa 
• Atom Count: 2,098 
• Modelled Residue Count: 260 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A	270	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names:  dapB, WHOK_00270, WHOK_02229C, WHOM_00688, WHOM_02238C, WHOP_00630, WHOP_02238C, WHOU_00751, WHOU_02311C, WHOV_01184, WHOV_02299C, WHOW_00218, WHOW_02292C, WHOX_00871, WHOX_02228C, WHOY_00570, WHOY_02311C, WHOZ_01787, WHOZ_02300C EC: 1.17.1.8
UniProt
Find proteins for Q5F5Y7 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F5Y7  Go to UniProtKB:  Q5F5Y7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.803	α = 90
b = 71.723	β = 90
c = 138.414	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
HKL-3000	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Pote, S.S., Pye, S.E., Sheahan, T.E., Chruszcz, M.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description