RCSB PDB - 5Z8K: Crystal structure of an aminotransferase in complex with product-1

 5Z8K

Crystal structure of an aminotransferase in complex with product-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.

Ban, Y.H.Song, M.C.Hwang, J.Y.Shin, H.L.Kim, H.J.Hong, S.K.Lee, N.J.Park, J.W.Cha, S.S.Liu, H.W.Yoon, Y.J.

(2019) Nat Chem Biol 15: 295-303

  • DOI: https://doi.org/10.1038/s41589-018-0203-4
  • Primary Citation of Related Structures:  
    5Z83, 5Z8A, 5Z8K

  • PubMed Abstract: 

    Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6'-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2'-deamination enzymes, limits GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6'-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.


  • Organizational Affiliation

    Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-6' aminotransferase
A, B
437Micromonospora echinosporaMutation(s): 0 
Gene Names: gacKgenB1gntW
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.847α = 90
b = 89.157β = 90
c = 117.364γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XXXClick on this verticalbar to view detailsBest fitted PLPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Oceans and FisheriesKorea, Republic Of20170305

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary