5F84 image
Deposition Date 2015-12-09
Release Date 2016-07-20
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5F84
Title:
Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
H 3 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:O-glucosyltransferase rumi
Gene (Uniprot):rumi
Chain IDs:A
Chain Length:402
Number of Molecules:1
Biological Source:Drosophila melanogaster
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Coagulation factor IX
Gene (Uniprot):F9
Chain IDs:B
Chain Length:50
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations.
Nat. Chem. Biol. 12 735 740 (2016)
PMID: 27428513 DOI: 10.1038/nchembio.2135

Abstact

Rumi O-glucosylates the EGF repeats of a growing list of proteins essential in metazoan development, including Notch. Rumi is essential for Notch signaling, and Rumi dysregulation is linked to several human diseases. Despite Rumi's critical roles, it is unknown how Rumi glucosylates a serine of many but not all EGF repeats. Here we report crystal structures of Drosophila Rumi as binary and ternary complexes with a folded EGF repeat and/or donor substrates. These structures provide insights into the catalytic mechanism and show that Rumi recognizes structural signatures of the EGF motif, the U-shaped consensus sequence, C-X-S-X-(P/A)-C and a conserved hydrophobic region. We found that five Rumi mutations identified in cancers and Dowling-Degos disease are clustered around the enzyme active site and adversely affect its activity. Our study suggests that loss of Rumi activity may underlie these diseases, and the mechanistic insights may facilitate the development of modulators of Notch signaling.

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Primary Citation of related structures