3DI0 | pdb_00003di0

Crystal Structure of Dihydrodipicolinate synthase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3DI0/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-19 Released: 2008-08-12 
• Deposition Author(s): Tavarekere, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.250 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of Staphylococcus aureus dihydrodipicolinate synthase

Girish, T.S., Sharma, E., Gopal, B.

(2008) FEBS Lett 582: 2923-2930

• PubMed: 18671976 
• DOI: https://doi.org/10.1016/j.febslet.2008.07.035
• Primary Citation Related Structures: 
  3DI0, 3DI1


• PubMed Abstract: 
  

  Lysine biosynthesis is crucial for cell-wall formation in bacteria. Enzymes involved in lysine biosynthesis are thus potential targets for anti-microbial therapeutics. Dihydrodipicolinate synthase (DHDPS) catalyzes the first step of this pathway. Unlike its homologues, Staphylococcus aureus DHDPS is a dimer both in solution and in the crystal and is not feedback inhibited by lysine. The crystal structure of S. aureus DHDPS in the free and substrate bound forms provides a structural rationale for its catalytic mechanism. The structure also reveals unique conformational features of the S. aureus enzyme that could be crucial for the design of specific non-competitive inhibitors.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 65.41 kDa 
• Atom Count: 4,678 
• Modeled Residue Count: 583 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	295	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: DHDPS EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q5HG25 (Staphylococcus aureus (strain COL)) Explore Q5HG25  Go to UniProtKB:  Q5HG25

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.250 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.686	α = 90
b = 118.686	β = 90
c = 179.156	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Tavarekere, G.S.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description