3TUU

Structure of dihydrodipicolinate synthase from the common grapevine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine.

Atkinson, S.C., Dogovski, C., Downton, M.T., Pearce, F.G., Reboul, C.F., Buckle, A.M., Gerrard, J.A., Dobson, R.C., Wagner, J., Perugini, M.A.

(2012) PLoS One 7: e38318-e38318

  • DOI: 10.1371/journal.pone.0038318
  • Primary Citation of Related Structures:  
    3TUU

  • PubMed Abstract: 

    • Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers ...

    Dihydrodipicolinate synthase (DHDPS) catalyzes the rate limiting step in lysine biosynthesis in bacteria and plants. The structure of DHDPS has been determined from several bacterial species and shown in most cases to form a homotetramer or dimer of dimers. However, only one plant DHDPS structure has been determined to date from the wild tobacco species, Nicotiana sylvestris (Blickling et al. (1997) J. Mol. Biol. 274, 608-621). Whilst N. sylvestris DHDPS also forms a homotetramer, the plant enzyme adopts a 'back-to-back' dimer of dimers compared to the 'head-to-head' architecture observed for bacterial DHDPS tetramers. This raises the question of whether the alternative quaternary architecture observed for N. sylvestris DHDPS is common to all plant DHDPS enzymes. Here, we describe the structure of DHDPS from the grapevine plant, Vitis vinifera, and show using analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography that V. vinifera DHDPS forms a 'back-to-back' homotetramer, consistent with N. sylvestris DHDPS. This study is the first to demonstrate using both crystal and solution state measurements that DHDPS from the grapevine plant adopts an alternative tetrameric architecture to the bacterial form, which is important for optimizing protein dynamics as suggested by molecular dynamics simulations reported in this study.

    Organizational Affiliation: 

    Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dihydrodipicolinate synthase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
346Vitis viniferaMutation(s): 0 
Gene Names: VIT_15s0048g00750
EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for D7U7T8 (Vitis vinifera)
Explore D7U7T8 
Go to UniProtKB:  D7U7T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7U7T8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR
Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H],
I [auth A],
J [auth A],
L [auth B],
AA [auth G],
DA [auth H],
I [auth A],
J [auth A],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
V [auth F],
W [auth F],
Y [auth G],
Z [auth G]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
BA [auth G],
CA [auth G],
EA [auth H],
K [auth A],
M [auth B],
BA [auth G],
CA [auth G],
EA [auth H],
K [auth A],
M [auth B],
P [auth C],
U [auth E],
X [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.55α = 93.19
b = 78.9β = 95.02
c = 135.35γ = 100.61
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release