4Q85

YcaO with Non-hydrolyzable ATP (AMPCPP) Bound

Summary for 4Q85

• Entry DOI: 10.2210/pdb4q85/pdb
• Related: 4q84 4q86
• Descriptor: Ribosomal protein S12 methylthiotransferase accessory factor YcaO, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: ycao atp binding domain, protein binding
• Biological source: Escherichia coli
• Total number of polymer chains: 8
• Total formula weight: 528604.71

Authors

Chekan, J.R.,Nair, S.K. (deposition date: 2014-04-25, release date: 2014-08-13, Last modification date: 2024-02-28)

Primary citation

Dunbar, K.L.,Chekan, J.R.,Cox, C.L.,Burkhart, B.J.,Nair, S.K.,Mitchell, D.A.
Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis.
Nat.Chem.Biol., 10:823-829, 2014

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. 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.

PubMed: 25129028
DOI: 10.1038/nchembio.1608

Experimental method

X-RAY DIFFRACTION (3.29 Å)