6CBO

X-ray structure of GenB1 from micromonospora echinospora in complex with neamine and PLP (as the external aldimine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin.

Dow, G.T.Thoden, J.B.Holden, H.M.

(2018) Protein Sci 27: 945-956

  • DOI: 10.1002/pro.3400
  • Primary Citation of Related Structures:  
    6CBK, 6CBL, 6CBM, 6CBN, 6CBO

  • PubMed Abstract: 
  • The aminoglycoside antibiotics, discovered as natural products in the 1940s, demonstrate a broad antimicrobial spectrum. Due to their nephrotoxic and ototoxic side effects, however, their widespread clinical usage has typically been limited to the treatment of serious infections ...

    The aminoglycoside antibiotics, discovered as natural products in the 1940s, demonstrate a broad antimicrobial spectrum. Due to their nephrotoxic and ototoxic side effects, however, their widespread clinical usage has typically been limited to the treatment of serious infections. Neomycin B, first isolated from strains of Streptomyces in 1948, is one such drug that was approved for human use by the U.S. Food and Drug Administration in 1964. Only within the last 11 years has the biochemical pathway for its production been elaborated, however. Here we present the three-dimensional architecture of NeoB from Streptomyces fradiae, which is a pyridoxal 5'-phosphate or PLP-dependent aminotransferase that functions on two different substrates in neomycin B biosynthesis. For this investigation, four high resolution X-ray structures of NeoB were determined in various complexed states. The overall fold of NeoB is that typically observed for members of the "aspartate aminotransferase" family with the exception of an additional three-stranded antiparallel β-sheet that forms part of the subunit-subunit interface of the dimer. The manner in which the active site of NeoB accommodates quite different substrates has been defined by this investigation. In addition, during the course of this study, we also determined the structure of the aminotransferase GenB1 to high resolution. GenB1 functions as an aminotransferase in gentamicin biosynthesis. Taken together, the structures of NeoB and GenB1, presented here, provide the first detailed descriptions of aminotransferases that specifically function on aldehyde moieties in aminoglycoside biosynthesis.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, WI, 53706.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-6' aminotransferaseA, B, C, D439Micromonospora echinosporaMutation(s): 0 
Gene Names: gacKgenB1gntWJD80_03676
UniProt
Find proteins for Q70KD9 (Micromonospora echinospora)
Explore Q70KD9 
Go to UniProtKB:  Q70KD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70KD9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOW
Query on DOW

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
O [auth D]
(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranoside
C20 H36 N5 O11 P
YAANPRCSTYUZOJ-GMRNZWOESA-N
 Ligand Interaction
MPO
Query on MPO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
P [auth D],
Q [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
N [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.888α = 90
b = 59.98β = 95.19
c = 210.694γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data 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: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-21
    Changes: Database references
  • Version 1.3: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence