5TEN

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5 Furan Dicarboxylic and NADH with Intact Polyhistidine Tag

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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This is version 1.3 of the entry. See complete history. 


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

  • 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.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate reductase
A, B, C, D, E
A, B, C, D, E, F, G, H
269Vibrio vulnificus CMCP6Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DEM0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
DA [auth F]
I [auth A]
IA [auth G]
MA [auth H]
N [auth B]
DA [auth F],
I [auth A],
IA [auth G],
MA [auth H],
N [auth B],
Q [auth C],
W [auth D],
Z [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
7FN
Query on 7FN
Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
JA [auth G]
NA [auth H]
O [auth B]
AA [auth E],
EA [auth F],
JA [auth G],
NA [auth H],
O [auth B],
R [auth C],
V [auth C],
X [auth D]
2,5 Furan Dicarboxylic Acid
C6 H4 O5
CHTHALBTIRVDBM-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
FA [auth F]
GA [auth F]
HA [auth F]
BA [auth E],
CA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
J [auth A],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth A],
OA [auth H],
P [auth B],
PA [auth H],
QA [auth H],
S [auth C],
T [auth C],
U [auth C],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.439α = 90
b = 117.545β = 92.19
c = 131.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

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: 2017-10-25
    Changes: Source and taxonomy
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description