6U01 | pdb_00006u01

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6U01

This is version 1.3 of the entry. See complete history

Literature

Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.

Majdi Yazdi, M.Saran, S.Mrozowich, T.Lehnert, C.Patel, T.R.Sanders, D.A.R.Palmer, D.R.J.

(2020) J Struct Biol 209: 107409-107409

  • DOI: https://doi.org/10.1016/j.jsb.2019.107409
  • Primary Citation Related Structures: 
    6TZU, 6U01

  • PubMed Abstract: 

    Dihydrodipicolinate synthase (DHDPS) from Campylobacter jejuni is a natively homotetrameric enzyme that catalyzes the first unique reaction of (S)-lysine biosynthesis and is feedback-regulated by lysine through binding to an allosteric site. High-resolution structures of the DHDPS-lysine complex have revealed significant insights into the binding events. One key asparagine residue, N84, makes hydrogen bonds with both the carboxyl and the α-amino group of the bound lysine. We generated two mutants, N84A and N84D, to study the effects of these changes on the allosteric site properties. However, under normal assay conditions, N84A displayed notably lower catalytic activity, and N84D showed no activity. Here we show that these mutations disrupt the quaternary structure of DHDPS in a concentration-dependent fashion, as demonstrated by size-exclusion chromatography, multi-angle light scattering, dynamic light scattering, small-angle X-ray scattering (SAXS) and high-resolution protein crystallography.


  • Organizational Affiliation
    • Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada.

Macromolecule Content 

  • Total Structure Weight: 207.29 kDa 
  • Atom Count: 14,829 
  • Modeled Residue Count: 1,777 
  • Deposited Residue Count: 1,860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthase
A, B, C, D, E
A, B, C, D, E, F
310Campylobacter jejuniMutation(s): 1 
Gene Names: dapA_1dapAA6J93_04235C9J79_06575DDV78_09110EBI45_07605NCTC13362_01713
EC: 4.3.3.7
UniProt
Find proteins for Q9PPB4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168))
Explore Q9PPB4 
Go to UniProtKB:  Q9PPB4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PPB4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
H [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
AA [auth E],
O [auth B],
S [auth C],
W [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
JA [auth F]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
FA [auth F]
G [auth A]
GA [auth F]
HA [auth F]
IA [auth F]
FA [auth F],
G [auth A],
GA [auth F],
HA [auth F],
IA [auth F],
L [auth B],
M [auth B],
N [auth B],
R [auth C],
Y [auth E],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
CA [auth E]
P [auth B]
T [auth C]
U [auth C]
V [auth C]
CA [auth E],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth F]
EA [auth F]
I [auth B]
J [auth B]
K [auth B]
DA [auth F],
EA [auth F],
I [auth B],
J [auth B],
K [auth B],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KPI
Query on KPI
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H16 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.99α = 90
b = 231.42β = 90
c = 200.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
HKL-3000data collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-29
    Changes: Data collection