6VW4

2.35 Angstrom structure of Caci_6494 from Catenulispora Acidiphila in complex with S-DNPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

Currently 6VW4 does not have a validation slider image.


This is version 1.4 of the entry. See complete history


Literature

Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis.

Vuksanovic, N.Zhu, X.Serrano, D.A.Siitonen, V.Metsa-Ketela, M.Melancon 3rd, C.E.Silvaggi, N.R.

(2020) Acta Crystallogr F Struct Biol Commun 76: 372-383

  • DOI: https://doi.org/10.1107/S2053230X20009814
  • Primary Citation of Related Structures:  
    5BKA, 6P77, 6P7L, 6VW4

  • PubMed Abstract: 

    Proteins belonging to the NTF2-like superfamily are present in the biosynthetic pathways of numerous polyketide natural products, such as anthracyclins and benzoisochromanequinones. Some have been found to be bona fide polyketide cyclases, but many of them have roles that are currently unknown. Here, the X-ray crystal structures of three NTF2-like proteins of unknown function are reported: those of ActVI-ORFA from Streptomyces coelicolor A3(2) and its homologs Caci_6494, a protein from an uncharacterized biosynthetic cluster in Catenulispora acidiphila, and Aln2 from Streptomyces sp. CM020, a protein in the biosynthetic pathway of alnumycin. The presence of a solvent-accessible cavity and the conservation of the His/Asp dyad that is characteristic of many polyketide cyclases suggest a potential enzymatic role for these enzymes in polyketide biosynthesis.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aromatic-ring-hydroxylating dioxygenase beta subunit
A, B
154Catenulispora acidiphila DSM 44928Mutation(s): 0 
Gene Names: Caci_6494
UniProt
Find proteins for C7PWR4 (Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908))
Explore C7PWR4 
Go to UniProtKB:  C7PWR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7PWR4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SDN (Subject of Investigation/LOI)
Query on SDN

Download Ideal Coordinates CCD File 
C [auth A][(3S)-9-hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetic acid
C16 H14 O5
HHXSOTFPYPQSBU-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.24α = 90
b = 161.24β = 90
c = 161.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report

Currently 6VW4 does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2020-09-02
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description