6BTD | pdb_00006btd

Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose

• PDB DOI: https://doi.org/10.2210/pdb6BTD/pdb

• Classification: LYASE
• Organism(s): Bacillus thuringiensis
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-12-06 Released: 2018-07-04 
• Deposition Author(s): Li, Q., Bruner, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.181 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Salvage of the 5-deoxyribose byproduct of radical SAM enzymes.

Beaudoin, G.A.W., Li, Q., Folz, J., Fiehn, O., Goodsell, J.L., Angerhofer, A., Bruner, S.D., Hanson, A.D.

(2018) Nat Commun 9: 3105-3105

• PubMed: 30082730 
• DOI: https://doi.org/10.1038/s41467-018-05589-4
• Primary Citation Related Structures: 
  6BTD, 6BTG


• PubMed Abstract: 
  

  5-Deoxyribose is formed from 5'-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, isomerization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5-deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite.

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Organizational Affiliation: 
• Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.
Biochemistry Department, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA. [e-mail].
Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.09 kDa 
• Atom Count: 1,802 
• Modeled Residue Count: 203 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fuculose phosphate aldolase	A	222	Bacillus thuringiensis	Mutation(s): 0  Gene Names: BK775_23715, CCZ40_07290 EC: 4.1.2.17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.181 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.724	α = 90
b = 103.724	β = 90
c = 48.817	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Li, Q., Bruner, S.D.

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description