5ITW

Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Probing the influence of non-covalent contact networks identified by charge density analysis on the oxidoreductase BacC.

Perinbam, K.Balaram, H.Guru Row, T.N.Gopal, B.

(2017) Protein Eng. Des. Sel. 30: 265-272

  • DOI: 10.1093/protein/gzx006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillus subtilis BacC is an oxidoreductase involved in the biosynthesis of the potent antibiotic bacilysin. The crystal structure of BacC was determined at 1.19 Å resolution. An experimental charge density approach was used to calculate non-covalent ...

    Bacillus subtilis BacC is an oxidoreductase involved in the biosynthesis of the potent antibiotic bacilysin. The crystal structure of BacC was determined at 1.19 Å resolution. An experimental charge density approach was used to calculate non-covalent interactions within the monomer and across the dimeric interface of BacC. This interaction network, in turn, enabled an analysis of non-covalently connected paths that span the protein structure. One of the pathways of non-covalent interactions was examined by mutational analysis. Biochemical analysis of BacC mutants with potential disruptions in non-covalent interactions along this path revealed that residues that form nodes in pathways of non-covalent interactions influence catalytic activity more than others in a similar chemical environment. Furthermore, we note that nodes in the non-covalent interaction networks are co-localized with compensatory mutation sites identified by multiple sequence alignment of proteins with low sequence similarity to BacC. Put together, this analysis supports the hypothesis that non-covalent nodes represent conserved structural features that can impact the catalytic activity of an enzyme.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroanticapsin 7-dehydrogenase
A, B, C, D
255Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: bacC (ywfD)
EC: 1.1.1.385
Find proteins for P39640 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39640
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.520α = 90.00
b = 87.200β = 101.08
c = 78.290γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific and Industrial ResearchIndia--
Department Of Science & TechnologyIndia--

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references