4Q84

Apo YcaO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis.

Dunbar, K.L.Chekan, J.R.Cox, C.L.Burkhart, B.J.Nair, S.K.Mitchell, D.A.

(2014) Nat.Chem.Biol. 10: 823-829

  • DOI: 10.1038/nchembio.1608
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Despite intensive research, the cyclodehydratase responsible for azoline biogenesis in thiazole/oxazole-modified microcin (TOMM) natural products remains enigmatic. The collaboration of two proteins, C and D, is required for cyclodehydration. The C p ...

    Despite intensive research, the cyclodehydratase responsible for azoline biogenesis in thiazole/oxazole-modified microcin (TOMM) natural products remains enigmatic. The collaboration of two proteins, C and D, is required for cyclodehydration. The C protein is homologous to E1 ubiquitin-activating enzymes, whereas the D protein is within the YcaO superfamily. Recent studies have demonstrated that TOMM YcaOs phosphorylate amide carbonyl oxygens to facilitate azoline formation. Here we report the X-ray crystal structure of an uncharacterized YcaO from Escherichia coli (Ec-YcaO). Ec-YcaO harbors an unprecedented fold and ATP-binding motif. This motif is conserved among TOMM YcaOs and is required for cyclodehydration. Furthermore, we demonstrate that the C protein regulates substrate binding and catalysis and that the proline-rich C terminus of the D protein is involved in C protein recognition and catalysis. This study identifies the YcaO active site and paves the way for the characterization of the numerous YcaO domains not associated with TOMM biosynthesis.


    Organizational Affiliation

    1] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3].,1] Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2].,1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,1] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S12 methylthiotransferase accessory factor YcaO
A, B
586Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ycaO
Find proteins for P75838 (Escherichia coli (strain K12))
Go to UniProtKB:  P75838
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.946α = 90.00
b = 140.386β = 90.00
c = 163.345γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references