4GZ3

Crystal structure of human O-GlcNAc Transferase with UDP and a thioglycopeptide

PDB DOI: https://doi.org/10.2210/pdb4GZ3/pdb

Classification: transferase/peptide
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-05 Released: 2012-10-31
Deposition Author(s): Lazarus, M.B., Jiang, J., Gloster, T.M., Zandberg, W.F., Vocadlo, D.J., Walker, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.250
R-Value Work: 0.226
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural snapshots of the reaction coordinate for O-GlcNAc transferase.

Lazarus, M.B., Jiang, J., Gloster, T.M., Zandberg, W.F., Whitworth, G.E., Vocadlo, D.J., Walker, S.

(2012) Nat Chem Biol 8: 966-968

PubMed: 23103939 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nchembio.1109
Primary Citation of Related Structures:
4GYW, 4GYY, 4GZ3, 4GZ5, 4GZ6

PubMed Abstract:
Visualization of the reaction coordinate undertaken by glycosyltransferases has remained elusive but is critical for understanding this important class of enzyme. Using substrates and substrate mimics, we describe structural snapshots of all species along the kinetic pathway for human O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase), an intracellular enzyme that catalyzes installation of a dynamic post-translational modification. The structures reveal key features of the mechanism and show that substrate participation is important during catalysis.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 166.32 kDa
Atom Count: 12,010
Modelled Residue Count: 1,397
Deposited Residue Count: 1,474
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	723	Homo sapiens	Mutation(s): 0 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
Casein kinase II subunit alpha	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
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]
0YT Query on 0YT 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-5-thio-beta-D-glucopyranose C₈ H₁₅ N O₅ S DYCCLPFFILCZGU-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]

Binding Affinity Annotations
ID	Source	Binding Affinity
UDP	BindingDB: 4GZ3	IC50: 1800 (nM) from 1 assay(s)
UDP	PDBBind: 4GZ3	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.250
R-Value Work: 0.226
R-Value Observed: 0.227
Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.77	α = 90
b = 137.62	β = 102.82
c = 153.016	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-10-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-31
Type: Initial release
Version 1.1: 2012-12-12
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Structure summary