Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 99.79 kDa 
• Atom Count: 6931 
• Modelled Residue Count: 822 
• Deposited Residue Count: 880 
• Unique protein chains: 1

5W71

X-ray structure of BtrR from Bacillus circulans in the presence of the 2-DOS external aldimine

• PDB DOI: 10.2210/pdb5W71/pdb

• Classification: TRANSFERASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-19 Released: 2017-07-12 
• Deposition Author(s): Zachman-Brockmeyer, T.R., Thoden, J.B., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

The structure of RbmB from Streptomyces ribosidificus, an aminotransferase involved in the biosynthesis of ribostamycin.

Zachman-Brockmeyer, T.R., Thoden, J.B., Holden, H.M.

(2017) Protein Sci 26: 1886-1892

• PubMed: 28685903 
• DOI: 10.1002/pro.3221
• Primary Citation of Related Structures:  
  5W70, 5W71


• PubMed Abstract: 
  

Aminoglycoside antibiotics represent a classical group of antimicrobials first discovered in the 1940s. Due to their ototoxic and nephrotoxic side effects, they are typically only used against Gram negative bacteria which have become resistant to other therapeutics. One family of aminoglycosides includes such compounds as butirosin, ribostamycin, neomycin, and kanamycin, amongst others. The common theme in these antibiotics is that they are constructed around a chemically stable aminocyclitol unit referred to as 2-deoxystreptamine (2-DOS). Four enzymes are required for the in vivo production of 2-DOS. Here, we report the structure of RbmB from Streptomyces ribosidificus, which is a pyridoxal 5'-phosphate dependent enzyme that catalyzes two of the required steps in 2-DOS formation by functioning on distinct substrates. For this analysis, the structure of the external aldimine form of RbmB with 2-DOS was determined to 2.1 Å resolution. In addition, the structure of a similar enzyme, BtrR from Bacillus circulans, was also determined to 2.1 Å resolution in the same external aldimine form. These two structures represent the first detailed molecular descriptions of the active sites for those aminotransferases involved in 2-DOS production. Given the fact that the 2-DOS unit is widespread amongst aminoglycoside antibiotics, the data presented herein provide new molecular insight into the biosynthesis of these sugar-based drugs.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-glutamine:2-deoxy-scyllo-inosose aminotransferase	A, B	440	Niallia circulans	Mutation(s): 0  Gene Names: btrR, btrS EC: 2.6.1.100 (PDB Primary Data), 2.6.1.101 (PDB Primary Data)
UniProt
Find proteins for Q8G8Y2 (Niallia circulans) Explore Q8G8Y2  Go to UniProtKB:  Q8G8Y2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YM	D [auth B]	[4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate C14 H24 N3 O8 P QHLVFXGQUJCQEL-MYALOSSISA-N
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.4	α = 90
b = 74.8	β = 90
c = 180.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-19 
• Released Date: 2017-07-12 
Deposition Author(s): Zachman-Brockmeyer, T.R., Thoden, J.B., Holden, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115921

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-07-19
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence