1TUW | pdb_00001tuw

Structural and Functional Analysis of Tetracenomycin F2 Cyclase from Streptomyces glaucescens: A Type-II Polyketide Cyclase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.245 (Depositor) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase.

Thompson, T.B.Katayama, K.Watanabe, K.Hutchinson, C.R.Rayment, I.

(2004) J Biological Chem 279: 37956-37963

  • DOI: https://doi.org/10.1074/jbc.M406144200
  • Primary Citation Related Structures: 
    1TUW

  • PubMed Abstract: 

    Tetracenomycin F2 cyclase (tcmI gene product), catalyzes an aromatic rearrangement in the biosynthetic pathway for tetracenomycin C in Streptomyces glaucescens. The x-ray structure of this small enzyme has been determined to 1.9-A resolution together with an analysis of site-directed mutants of potential catalytic residues. The protein exhibits a dimeric betaalphabeta ferredoxin-like fold that utilizes strand swapping between subunits in its assembly. The fold is dominated by four strands of antiparallel sheet and a layer of alpha-helices, which creates a cavity that is proposed to be the active site. This type of secondary structural arrangement has been previously observed in polyketide monooxygenases and suggests an evolutionary relationship between enzymes that catalyze adjacent steps in these biosynthetic pathways. Mutational analysis of all of the obvious catalytic bases within the active site suggests that the enzyme functions to steer the chemical outcome of the cyclization rather than providing a specific catalytic group. Together, the structure and functional analysis provide insight into the structural framework necessary to perform the complex rearrangements catalyzed by this class of polyketide cyclases.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 12.97 kDa 
  • Atom Count: 934 
  • Modeled Residue Count: 106 
  • Deposited Residue Count: 109 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tetracenomycin polyketide synthesis protein tcmI109Streptomyces glaucescensMutation(s): 0 
Gene Names: TCMI
EC: 4.2.1.154
UniProt
Find proteins for P39890 (Streptomyces glaucescens)
Explore P39890 
Go to UniProtKB:  P39890
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39890
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.245 (Depositor) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.7α = 90
b = 46.7β = 90
c = 188.3γ = 120
Software Package:
Software NamePurpose
Histardata collection
XDSdata reduction
SOLVEphasing
TNTrefinement
HISTARdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations