4G3M

Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 

Starting Model: experimental
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Literature

Evolution of vitamin B(2) biosynthesis: eubacterial RibG and fungal Rib2 deaminases.

Chen, S.C.Shen, C.Y.Yen, T.M.Yu, H.C.Chang, T.H.Lai, W.L.Liaw, S.H.

(2013) Acta Crystallogr D Biol Crystallogr 69: 227-236

  • DOI: https://doi.org/10.1107/S0907444912044903
  • Primary Citation of Related Structures:  
    4G3M

  • PubMed Abstract: 

    Eubacterial RibG and yeast Rib2 possess a deaminase domain for pyrimidine deamination in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for ribose and ribitol, respectively. Here, the crystal structure of Bacillus subtilis RibG in complex with a deaminase product is reported at 2.56 Å resolution. Two loops move towards the product on substrate binding, resulting in interactions with the ribosyl and phosphate groups and significant conformational changes. The product carbonyl moiety is bent out of the pyrimidine ring to coordinate to the catalytic zinc ion. Such distortions in the bound substrate and product may play an essential role in enzyme catalysis. The yeast Rib2 structure was modelled and a mutational analysis was carried out in order to understand the mechanism of substrate recognition in these two enzymes. Detailed structural comparisons revealed that the two consecutive carbonyl backbones that occur prior to the PCXXC signature constitute a binding hole for the target amino group of the substrate. This amino-binding hole is essential in B. subtilis RibG and is also conserved in the RNA/DNA-editing deaminases.


  • Organizational Affiliation

    Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Riboflavin biosynthesis protein RibD
A, B, C, D
373Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU23280ribDribG
EC: 3.5.4.26 (PDB Primary Data), 1.1.1.193 (PDB Primary Data)
UniProt
Find proteins for P17618 (Bacillus subtilis (strain 168))
Explore P17618 
Go to UniProtKB:  P17618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17618
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AOF
Query on AOF

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C],
N [auth D]
N-(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine
C9 H15 N4 O9 P
LZEXYCAGPMYXLX-UMMCILCDSA-N
AI9
Query on AI9

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
[(2R,3S,4S,5E)-5-[[5-azanyl-2,4-bis(oxidanylidene)-1H-pyrimidin-6-yl]imino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate
C9 H15 N4 O9 P
XKTZRTIKRCUGRX-ODDLNGBBSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.014α = 90
b = 109.19β = 90
c = 189.472γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description