6TZU

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site

• PDB DOI:  https://doi.org/10.2210/pdb6TZU/pdb

• Classification: LYASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-13 Released: 2019-12-04 
• Deposition Author(s): Saran, S., Majdi Yazdi, M., Lehnert, C., Palmer, D.R.J., Sanders, D.A.R.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

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

• PubMed: 31678256 
• DOI: https://doi.org/10.1016/j.jsb.2019.107409
• Primary Citation of 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. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 208.27 kDa 
• Atom Count: 15,399 
• Modelled Residue Count: 1,795 
• Deposited Residue Count: 1,860 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 1  Gene Names: dapA, Cj0806 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	F	310	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 1  Gene Names: dapA, Cj0806 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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	IB [auth F], N [auth A], NA [auth D], Y [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	EA [auth C], FA [auth C], X [auth B], YA [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	OA [auth D], ZA [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	BB [auth F], CB [auth F], DB [auth F], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], MA [auth D], P [auth B], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EB [auth F], FB [auth F], GB [auth F], HB [auth F], M [auth A], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], XA [auth E], Z [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	AB [auth F], G [auth A], H [auth A], O [auth B], PA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	F	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.93	α = 90
b = 225.81	β = 90
c = 200.74	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XSCALE	data scaling
HKL-3000	data collection
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Saran, S., Majdi Yazdi, M., Lehnert, C., Palmer, D.R.J., Sanders, D.A.R.

---

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references