4Q86

YcaO with AMP Bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


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:  
    4Q84, 4Q85, 4Q86

  • 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 protein is homologous to E1 ubiquitin-activating enzymes, whereas the D protein is within the YcaO superfamily ...

    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] 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S12 methylthiotransferase accessory factor YcaO
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
586Escherichia coli K-12Mutation(s): 0 
Gene Names: ycaO, b0905, JW0888
UniProt
Find proteins for P75838 (Escherichia coli (strain K12))
Explore P75838 
Go to UniProtKB:  P75838
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75838
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
CA [auth G],
GA [auth H],
I [auth A],
M [auth B],
Q [auth C],
CA [auth G],
GA [auth H],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
DA [auth G],
EA [auth G],
FA [auth G],
AA [auth E],
BA [auth E],
DA [auth G],
EA [auth G],
FA [auth G],
HA [auth H],
IA [auth H],
J [auth A],
JA [auth H],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.254α = 89.94
b = 112.949β = 73.51
c = 132.886γ = 77.23
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
AutoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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