6IJ1

Crystal structure of a protein from Actinoplanes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of TchmY from Actinoplanes teichomyceticus.

Yang, Z.Zhang, L.Yu, X.Wu, S.Yang, Y.Hu, Y.Li, Q.Shang, N.Guo, R.T.Chen, C.C.Dai, L.Liu, W.

(2019) Acta Crystallogr F Struct Biol Commun 75: 570-575

  • DOI: https://doi.org/10.1107/S2053230X19010914
  • Primary Citation of Related Structures:  
    6IJ1

  • PubMed Abstract: 

    Moenomycin-type antibiotics are phosphoglycolipids that are notable for their unique modes of action and have proven to be useful in animal nutrition. The gene clusters tchm from Actinoplanes teichomyceticus and moe from Streptomyces are among a limited number of known moenomycin-biosynthetic pathways. Most genes in tchm have counterparts in the moe cluster, except for tchmy and tchmz, the functions of which remain unknown. Sequence analysis indicates that TchmY belongs to the isoprenoid enzyme C2-like superfamily and may serve as a prenylcyclase. The enzyme was proposed to be involved in terminal cyclization of the moenocinyl chain in teichomycin, leading to the diumycinol chain of moenomycin isomers. Here, recombinant TchmY protein was expressed in Escherichia coli and its crystal structure was solved by SIRAS. Structural analysis and comparison with other prenylcyclases were performed. The overall fold of TchmY consists of an (α/α) 6 -barrel, and a potential substrate-binding pocket is found in the central chamber. These results should provide important information regarding the biosynthetic basis of moenomycin antibiotics.


  • Organizational Affiliation

    College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prenylcyclase346Actinoplanes teichomyceticusMutation(s): 0 
Gene Names: tchmY
UniProt
Find proteins for A0A1B1ESM0 (Actinoplanes teichomyceticus)
Explore A0A1B1ESM0 
Go to UniProtKB:  A0A1B1ESM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B1ESM0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.471α = 90
b = 73.471β = 90
c = 124.234γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references