PDBsum entry 5f84

Transferase/hydrolase

PDB id: 5f84

Contents

Protein chains

365 a.a.

39 a.a.

Ligands

UDP

SO4 ×5

BGC

Waters ×95

PDB id:

5f84

Name:

Transferase/hydrolase

Title:

Crystal structure of drosophila poglut1 (rumi) complexed with its glycoprotein product (glucosylated egf repeat) and udp

Structure:

O-glucosyltransferase rumi. Chain: a. Fragment: unp residues 21-407. Engineered: yes. Coagulation factor ix. Chain: b. Fragment: unp residues 92-130. Synonym: christmas factor,plasma thromboplastin component,ptc. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: rumi, cg31152. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293t. Homo sapiens. Human.

Resolution:

2.50Å R-factor: 0.194 R-free: 0.239

Authors:

H.J.Yu,H.L.Li

Key ref:

H.Yu et al. (2016). Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations. Nat Chem Biol, 12, 735-740. PubMed id: 27428513

Date:

09-Dec-15 Release date: 20-Jul-16

Protein chain

Q8T045  (RUMI_DROME) -  O-glucosyltransferase rumi from Drosophila melanogaster

Seq: 411 a.a.

Struc: 365 a.a.

Protein chain

P00740  (FA9_HUMAN) -  Coagulation factor IX from Homo sapiens

Seq: 461 a.a.

Struc: 39 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chain A: E.C.2.4.1.- - ?????
• Enzyme class 2: Chain B: E.C.3.4.21.22 - coagulation factor IXa.
• Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Nat Chem Biol 12:735-740 (2016)

PubMed id: 27428513

Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations.

H.Yu, H.Takeuchi, M.Takeuchi, Q.Liu, J.Kantharia, R.S.Haltiwanger, H.Li.

ABSTRACT

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.