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)

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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 

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 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 4 generated by PISA (software)

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

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 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
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	E [auth A], I [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	G [auth B], J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A], H [auth B], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
UDP	BindingDB:  5HGV	IC50: 1800 (nM) from 1 assay(s)

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

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Janetzko, J., Lazarus, M.B., Walker, S.

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

Revision History  

• 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