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)

Macromolecule Content

• Total Structure Weight: 63.29 kDa 
• Atom Count: 4,892 
• Modelled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

 4EOU

Crystal structure of E. coli dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

• PDB DOI: 10.2210/pdb4EOU/pdb
• Entry: 4EOU supersedes: 3UBS

• Classification: LYASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-15 Released: 2012-04-25 
• Deposition Author(s): Boughton, B.A., Dobson, R.C.J., Hutton, C.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.198 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 

Literature

The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: Unambiguous resolution of the stereochemistry of the condensation product.

Boughton, B.A., Dobson, R.C., Hutton, C.A.

(2012) Proteins 80: 2117-2122

• PubMed: 22552955 
• DOI: 10.1002/prot.24106
• Primary Citation of Related Structures:  
  4EOU


• PubMed Abstract: 
  

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures.

---

Organizational Affiliation: 

School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	292	Escherichia coli	Mutation(s): 0  EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2  Go to UniProtKB:  P0A6L2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	C [auth A], E [auth A], F [auth B], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LYF	A, B	L-PEPTIDE LINKING	C13 H22 N2 O7		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.198 
• R-Value Work: 0.143 
• R-Value Observed: 0.146 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.172	α = 90
b = 121.172	β = 90
c = 109.732	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Boughton, B.A., Dobson, R.C.J., Hutton, C.A.
• This entry supersedes: 3UBS

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Database references
• Version 1.2: 2012-07-25
  Changes: Database references