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

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate reductaseA [auth C],
B [auth A]
269Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: dapBVV1_0567
Find proteins for Q8DEM0 (Vibrio vulnificus (strain CMCP6))
Explore Q8DEM0 
Go to UniProtKB:  Q8DEM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DEM0
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • 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 = 80.639α = 90
b = 112.588β = 90
c = 62.432γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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