5HGV

Structure of an O-GlcNAc transferase point mutant, D554N in complex with peptide

PDB DOI: https://doi.org/10.2210/pdb5HGV/pdb

Classification: TRANSFERASE/PEPTIDE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-01-08 Released: 2016-09-14
Deposition Author(s): Janetzko, J., Lazarus, M.B., Walker, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.217
R-Value Observed: 0.218

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

How the glycosyltransferase OGT catalyzes amide bond cleavage.

Janetzko, J., Trauger, S.A., Lazarus, M.B., Walker, S.

(2016) Nat Chem Biol 12: 899-901

PubMed: 27618188 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nchembio.2173
Primary Citation of Related Structures:
5HGV

PubMed Abstract:
The essential human enzyme O-linked β-N-acetylglucosamine transferase (OGT), known for modulating the functions of nuclear and cytoplasmic proteins through serine and threonine glycosylation, was unexpectedly implicated in the proteolytic maturation of the cell cycle regulator host cell factor-1 (HCF-1). Here we show that HCF-1 cleavage occurs via glycosylation of a glutamate side chain followed by on-enzyme formation of an internal pyroglutamate, which undergoes spontaneous backbone hydrolysis.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Macromolecule Content

Total Structure Weight: 165.69 kDa
Atom Count: 11,958
Modelled Residue Count: 1,397
Deposited Residue Count: 1,466
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A, C	719	Homo sapiens	Mutation(s): 1 Gene Names: OGT EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens) Explore O15294 Go to UniProtKB: O15294
PHAROS: O15294 GTEx: ENSG00000147162
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15294
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET	B, D	14	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400 Go to UniProtKB: P68400
PHAROS: P68400 GTEx: ENSG00000101266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68400
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D	Go to GlyGen: P68400-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	F [auth A], H [auth B], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.217
R-Value Observed: 0.218
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.35	α = 90
b = 137.19	β = 103.05
c = 153.07	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
CBASS	data collection
iMOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Janetzko, J.

Lazarus, M.B.

Walker, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094263

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2016-10-26
Changes: Database references
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-10-30
Changes: Structure summary