5W71

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


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 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-glutamine:2-deoxy-scyllo-inosose aminotransferaseA, B440Niallia circulansMutation(s): 0 
Gene Names: btrRbtrS
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G8Y2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9YM
Query on 9YM

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 69.4α = 90
b = 74.8β = 90
c = 180.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115921

Revision History  (Full details and data files)

  • 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