1G57

CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE

• PDB DOI: https://doi.org/10.2210/pdb1G57/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-10-30 Released: 2001-04-30 
• Deposition Author(s): Liao, D.-I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V., Jordan, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.221 
• R-Value Work: 0.180 

Literature

Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis.

Liao, D.I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V., Jordan, D.B.

(2001) Structure 9: 11-18

• PubMed: 11342130 
• DOI: https://doi.org/10.1016/s0969-2126(00)00550-5
• Primary Citation of Related Structures:  
  1G57, 1G58


• PubMed Abstract: 
  

  3,4-Dihydroxy-2-butanone-4-phosphate synthase catalyzes a commitment step in the biosynthesis of riboflavin. On the enzyme, ribulose 5-phosphate is converted to 3,4-dihydroxy-2-butanone 4-phosphate and formate in steps involving enolization, ketonization, dehydration, skeleton rearrangement, and formate elimination. The enzyme is absent in humans and an attractive target for the discovery of antimicrobials for pathogens incapable of acquiring sufficient riboflavin from their hosts. The homodimer of 23 kDa subunits requires Mg(2+) for activity.

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Organizational Affiliation: 

DuPont Central Research and Development Experimental Station, Wilmington, DE 19880, USA. [e-mail]

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: 47.2 kDa 
• Atom Count: 3,527 
• Modelled Residue Count: 414 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE	A, B	217	Escherichia coli	Mutation(s): 0  EC: 5.4.99
UniProt
Find proteins for P0A7J0 (Escherichia coli (strain K12)) Explore P0A7J0  Go to UniProtKB:  P0A7J0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS	C [auth A], D [auth A], E [auth A], F [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.221 
• R-Value Work: 0.180 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.187	α = 90
b = 78.187	β = 90
c = 69.622	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-30 
Deposition Author(s): Liao, D.-I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V., Jordan, D.B.

Revision History  

• Version 1.0: 2001-04-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations