6VVH

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) in complex with lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.

Hall, C.J.Lee, M.Boarder, M.P.Mangion, A.M.Gendall, A.R.Panjikar, S.Perugini, M.A.Soares da Costa, T.P.

(2021) FEBS J 288: 4973-4986

  • DOI: https://doi.org/10.1111/febs.15766
  • Primary Citation of Related Structures:  
    6VVH, 6VVI

  • PubMed Abstract: 

    Lysine biosynthesis in plants occurs via the diaminopimelate pathway. The first committed and rate-limiting step of this pathway is catalysed by dihydrodipicolinate synthase (DHDPS), which is allosterically regulated by the end product, l-lysine (lysine). Given that lysine is a common nutritionally limiting amino acid in cereal crops, there has been much interest in probing the regulation of DHDPS. Interestingly, knockouts in Arabidopsis thaliana of each isoform (AtDHDPS1 and AtDHDPS2) result in different phenotypes, despite the enzymes sharing > 85% protein sequence identity. Accordingly, in this study, we compared the catalytic activity, lysine-mediated inhibition and structures of both A. thaliana DHDPS isoforms. We found that although the recombinantly produced enzymes have similar kinetic properties, AtDHDPS1 is 10-fold more sensitive to lysine. We subsequently used X-ray crystallography to probe for structural differences between the apo- and lysine-bound isoforms that could account for the differential allosteric inhibition. Despite no significant changes in the overall structures of the active or allosteric sites, we noted differences in the rotamer conformation of a key allosteric site residue (Trp116) and proposed that this could result in differences in lysine dissociation. Microscale thermophoresis studies supported our hypothesis, with AtDHDPS1 having a ~ 6-fold tighter lysine dissociation constant compared to AtDHDPS2, which agrees with the lower half minimal inhibitory concentration for lysine observed. Thus, we highlight that subtle differences in protein structures, which could not have been predicted from the primary sequences, can have profound effects on the allostery of a key enzyme involved in lysine biosynthesis in plants. DATABASES: Structures described are available in the Protein Data Bank under the accession numbers 6VVH and 6VVI.


  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplasticA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
321Arabidopsis thalianaMutation(s): 0 
Gene Names: DHDPS1DHDPSDHPS1At3g60880T4C21_290
EC: 4.3.3.7
UniProt
Find proteins for Q9LZX6 (Arabidopsis thaliana)
Explore Q9LZX6 
Go to UniProtKB:  Q9LZX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LZX6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
L [auth DDD]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
LYS (Subject of Investigation/LOI)
Query on LYS

Download Ideal Coordinates CCD File 
E [auth AAA],
H [auth BBB],
J [auth CCC],
O [auth DDD]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth BBB],
M [auth DDD],
N [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth AAA],
I [auth BBB],
K [auth CCC],
P [auth DDD]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.044α = 90
b = 97.626β = 90
c = 176.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE190100806

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary