Xylose isomerase 1F1 variant from Streptomyces sp. F-1

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes.

Miyamoto, R.Y.de Sousa, A.S.Vieira, P.S.de Melo, R.R.Scarpassa, J.A.Ramos, C.H.I.Murakami, M.T.Ruller, R.Zanphorlin, L.M.

(2020) Biochim Biophys Acta Gen Subj 1864: 129549-129549

  • DOI: https://doi.org/10.1016/j.bbagen.2020.129549
  • Primary Citation of Related Structures:  
    6N98, 6N99

  • PubMed Abstract: 

    Enzymatic isomerization is a promising strategy to solve the problem of xylose fermentation and, consequently, to leverage the production of advanced biofuels and biochemicals. In a previous work, our research group discovered a new strain of Streptomyces with great biotechnological potential due to its ability to produce a broad arsenal of enzymes related to lignocellulose degradation. We applied a multidisciplinary approach involving enzyme kinetics, biophysical methods, small angle X-ray scattering and X-ray crystallography to investigate two novel xylose isomerases, XylA1F1 and XylA2F1, from this strain. We showed that while XylA1F1 prefers to act at lower temperatures and relatively lower pH, XylA2F1 is extremely stable at higher temperatures and presents a higher turnover number. Structural analysis revealed that XylA1F1 exhibits unique properties in the active site not observed in classical XylAs from classes I and II nor in its ortholog XylA2F1. It encompasses the natural substitutions, M86A and T93K, that create an extra room for substrate accommodation and narrow the active-site entrance, respectively. Such modifications may contribute to the functional differentiation of these enzymes. We have characterized two novel xylose isomerases that display distinct functional behavior and harbor unprecedented amino-acid substitutions in the catalytic interface. Our findings contribute to a better understanding of the functional and structural aspects of xylose isomerases, which might be instrumental for the valorization of the hemicellulosic fraction of vegetal biomass.

  • Organizational Affiliation

    Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil; Institute of Biology, State University of Campinas, Campinas, SP, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase382Streptomyces sp. F-1Mutation(s): 0 
Gene Names: xylA_2xylASTEPF1_06097
Find proteins for A0A1K2FZ20 (Streptomyces sp. F-1)
Explore A0A1K2FZ20 
Go to UniProtKB:  A0A1K2FZ20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1K2FZ20
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.1α = 90
b = 92.9β = 90
c = 99.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2018/02865-2
Sao Paulo Research Foundation (FAPESP)Brazil2016/06509-0

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description