Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 138.99 kDa 
• Atom Count: 10,073 
• Modelled Residue Count: 1,190 
• Deposited Residue Count: 1,224 
• Unique protein chains: 1

 4LY8

dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site

• PDB DOI: 10.2210/pdb4LY8/pdb

• Classification: LYASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-30 Released: 2015-01-14 
• Deposition Author(s): Conly, C.J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine.

Conly, C.J., Skovpen, Y.V., Li, S., Palmer, D.R., Sanders, D.A.

(2014) Biochemistry 53: 7396-7406

• PubMed: 25369463 
• DOI: 10.1021/bi5012157
• Primary Citation of Related Structures:  
  4LY8, 4M19, 4MLJ, 4MLR, 4R53


• PubMed Abstract: 
  

Dihydrodipicolinate synthase (DHDPS), an enzyme found in most bacteria and plants, controls a critical step in the biosynthesis of l-lysine and meso-diaminopimelate, necessary components for bacterial cell wall biosynthesis. DHDPS catalyzes the condensation of pyruvate and (S)-aspartate-β-semialdehyde, forming an unstable product that is dehydrated to dihydrodipicolinate. The tetrameric enzyme is allosterically inhibited by l-lysine, and a better understanding of the allosteric inhibition mechanism is necessary for the design of potent antibacterial therapeutics. Here we describe the high-resolution crystal structures of DHDPS from Campylobacter jejuni with and without its inhibitor bound to the allosteric sites. These structures reveal a role for Y110 in the regulation of the allosteric inhibition by lysine. Mutation of Y110 to phenylalanine results in insensitivity to lysine inhibition, although the mutant crystal structure reveals that lysine does bind in the allosteric site. Comparison of the lysine-bound Y110F structure with wild-type structures reveals that key structural changes due to lysine binding are absent in this mutant.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D	306	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: Cj0806, dapA 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	CA [auth C], Q [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	F [auth A], FA [auth C], H [auth A], I [auth A], JA [auth C], K [auth A], LA [auth D], T [auth B], V [auth B], X [auth B], Y [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	MA [auth D], N [auth A], R [auth A], U [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], DA [auth C], E [auth A], EA [auth C], G [auth A], GA [auth C], HA [auth C], IA [auth C], J [auth A], M [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D], S [auth A], SA [auth D], TA [auth D], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	KA [auth C], L [auth A], P [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.254	α = 90
b = 101.404	β = 90
c = 147.96	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Conly, C.J.T.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release