PDBsum entry 5c1d

Transferase

PDB id: 5c1d

Contents

Protein chain

695 a.a.

Ligands

VAL-THR-PRO-VAL-SER-THR-ALA-ALA

12V

PO4 ×2

Waters ×254

PDB id:

5c1d

Name:

Transferase

Title:

Human ogt in complex with udp-5s-glcnac and substrate peptide (rb2l)

Structure:

Udp-n-acetylglucosamine--peptide n- acetylglucosaminyltransferase 110 kda subunit. Chain: a. Fragment: unp residues 313-1031. Synonym: o-glcnac transferase, o-glcnac transferase subunit p110,o- linked n-acetylglucosamine transferase 110 kda subunit,ogt. Engineered: yes. Retinoblastoma-like protein 2. Chain: c.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ogt. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Organism_taxid: 9606

Resolution:

2.05Å R-factor: 0.196 R-free: 0.229

Authors:

M.Schimpl,K.Rafie,D.M.F.Van Aalten

Key ref:

S.Pathak et al. (2015). The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nat Struct Biol, 22, 744-750. PubMed id: 26237509 DOI: 10.1038/nsmb.3063

Date:

13-Jun-15 Release date: 05-Aug-15

Protein chain

O15294  (OGT1_HUMAN) -  UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit from Homo sapiens

Seq: 1046 a.a.

Struc: 695 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.255 - protein O-GlcNAc transferase.
• Reaction:
  1. L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-(N-acetyl- beta-D-glucosaminyl)-L-seryl-[protein] + UDP + H⁺
  2. L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O- (N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + UDP + H⁺

L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-(N-acetyl- beta-D-glucosaminyl)-L-seryl-[protein] + UDP + H(+) (Bound ligand (Het Group name = 12V) matches with 64.10% similarity)

L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O- (N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + UDP + H(+) (Bound ligand (Het Group name = 12V) matches with 64.10% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/nsmb.3063

Nat Struct Biol 22:744-750 (2015)

PubMed id: 26237509

The active site of O-GlcNAc transferase imposes constraints on substrate sequence.

S.Pathak, J.Alonso, M.Schimpl, K.Rafie, D.E.Blair, V.S.Borodkin, A.W.Schüttelkopf, O.Albarbarawi, D.M.van Aalten.

ABSTRACT

O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoans. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay to a library of peptides. We mapped sites of O-GlcNAc modification by electron transfer dissociation MS and found that they correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with Homo sapiens OGT suggest that a combination of size and conformational restriction defines sequence specificity in the -3 to +2 subsites. This work reveals that although the N-terminal TPR repeats of OGT may have roles in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a substantial contribution to O-GlcNAc site specificity.