5TEM

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,6 Pyridine Dicarboxylic and NADH

• PDB DOI: https://doi.org/10.2210/pdb5TEM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-22 Released: 2017-10-18 
• Deposition Author(s): Mank, N., Arnette, K., Klapper, V., Chruszcz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.

Pote, S., Kachhap, S., Mank, N.J., Daneshian, L., Klapper, V., Pye, S., Arnette, A.K., Shimizu, L.S., Borowski, T., Chruszcz, M.

(2021) Biochim Biophys Acta Gen Subj 1865: 129750-129750

• PubMed: 32980502 
• DOI: https://doi.org/10.1016/j.bbagen.2020.129750
• Primary Citation of Related Structures:  
  5TEJ, 5TEK, 5TEM, 5TEN, 5TJY, 5TJZ, 5UGV, 5US6


• PubMed Abstract: 
  

  The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics.

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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)

Macromolecule Content

• Total Structure Weight: 59.39 kDa 
• Atom Count: 4,306 
• Modelled Residue Count: 532 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A [auth C], B [auth A]	269	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: dapB, VV1_0567 EC: 1.17.1.8
UniProt
Find proteins for Q8DEM0 (Vibrio vulnificus (strain CMCP6)) Explore Q8DEM0  Go to UniProtKB:  Q8DEM0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C, F [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PDC	D [auth C], G [auth A]	PYRIDINE-2,6-DICARBOXYLIC ACID C7 H5 N O4 WJJMNDUMQPNECX-UHFFFAOYSA-N
SO4	E [auth C], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.639	α = 90
b = 112.588	β = 90
c = 62.432	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Mank, N., Arnette, K., Klapper, V., Chruszcz, M.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description