4GZ6 | pdb_00004gz6

Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc

PDB DOI: https://doi.org/10.2210/pdb4GZ6/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-06 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: 2.98 Å
R-Value Free:
0.223 (Depositor), 0.222 (DCC)
R-Value Work:
0.197 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.1109
Primary Citation 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: 328.02 kDa
Atom Count: 22,407
Modeled Residue Count: 2,800
Deposited Residue Count: 2,892
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15294
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12V Query on 12V Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain E [auth A]	E [auth A], J [auth B], P [auth C], U [auth D]	(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate C₁₇ H₂₇ N₃ O₁₆ P₂ S JPRVHSQHWXZSNC-UBDZBXRQSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth B] F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.223 (Depositor), 0.222 (DCC)
R-Value Work: 0.197 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 272.338	α = 90
b = 272.338	β = 90
c = 143.46	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: 2024-02-28
Changes: Data collection, Database references, Derived calculations