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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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. We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction. Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD + , NADP + , as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism. This is the first report presenting the detailed mechanism of reaction catalyzed by DapB. Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (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: dapBVV1_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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Ligand Structure Quality Assessment 


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