9AUE

Crystal structure of the holo form of GenB2 in complex with PMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: in silico
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Literature

Structural and Functional Basis of GenB2 Isomerase Activity from Gentamicin Biosynthesis.

Oliveira, G.S.Dos S Bury, P.Huang, F.Li, Y.Araujo, N.C.Zhou, J.Sun, Y.Leeper, F.J.Leadlay, P.F.Dias, M.V.B.

(2024) ACS Chem Biol 19: 2002-2011

  • DOI: https://doi.org/10.1021/acschembio.4c00334
  • Primary Citation of Related Structures:  
    9AU3, 9AUE, 9B0C

  • PubMed Abstract: 

    Aminoglycosides are essential antibiotics used to treat severe infections caused mainly by Gram-negative bacteria. Gentamicin is an aminoglycoside and, despite its toxicity, is clinically used to treat several pulmonary and urinary infections. The commercial form of gentamicin is a mixture of five compounds with minor differences in the methylation of one of their aminosugars. In the case of two compounds, gentamicin C2 and C2a, the only difference is the stereochemistry of the methyl group attached to C-6'. GenB2 is the enzyme responsible for this epimerization and is one of the four PLP-dependent enzymes encoded by the gentamicin biosynthetic gene cluster. Herein, we have determined the structure of GenB2 in its holo form in complex with PMP and also in the ternary complex with gentamicin X2 and G418, two substrate analogues. Based on the structural analysis, we were able to identify the structural basis for the catalytic mechanism of this enzyme, which was also studied by site-directed mutagenesis. Unprecedently, GenB2 is a PLP-dependent enzyme from fold I, which is able to catalyze an epimerization but with a mechanism distinct from that of fold III PLP-dependent epimerases using a cysteine residue near the N-terminus. The substitution of this cysteine residue for serine or alanine completely abolished the epimerase function of the enzyme, confirming its involvement. This study not only contributes to the understanding of the enzymology of gentamicin biosynthesis but also provides valuable details for exploring the enzymatic production of new aminoglycoside derivatives.


  • Organizational Affiliation

    Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo 05508-000, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6'-epimerase, C-6' aminotransferase415Micromonospora echinosporaMutation(s): 0 
Gene Names: gacEgenB2gntL
UniProt
Find proteins for Q70KE6 (Micromonospora echinospora)
Explore Q70KE6 
Go to UniProtKB:  Q70KE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70KE6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.359α = 90
b = 103.752β = 90
c = 104.117γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2010/15971-3
Sao Paulo Research Foundation (FAPESP)Brazil2015/09188-8
Sao Paulo Research Foundation (FAPESP)Brazil2018/00351-1
Sao Paulo Research Foundation (FAPESP)Brazil2021/10577-0
Sao Paulo Research Foundation (FAPESP)Brazil2022/12234-5
Sao Paulo Research Foundation (FAPESP)Brazil2014/07843-6
Sao Paulo Research Foundation (FAPESP)Brazil2017/23627-0
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil208998/2020-0
National Natural Science Foundation of China (NSFC)China31920103001

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references