2VSN | pdb_00002vsn

Structure and topological arrangement of an O-GlcNAc transferase homolog: insight into molecular control of intracellular glycosylation

PDB DOI: https://doi.org/10.2210/pdb2VSN/pdb

Classification: TRANSFERASE
Organism(s): Xanthomonas campestris pv. campestris str. 8004
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2008-04-28 Released: 2008-06-10
Deposition Author(s): Martinez-Fleites, C., Macauley, M.S., He, Y., Shen, D., Vocadlo, D., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of an O-Glcnac Transferase Homolog Provides Insight Into Intracellular Glycosylation.

Martinez-Fleites, C., Macauley, M.S., He, Y., Shen, D.L., Vocadlo, D.J., Davies, G.J.

(2008) Nat Struct Mol Biol 15: 764

PubMed: 18536723 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1443
Primary Citation Related Structures:
2VSN

PubMed Abstract:
N-Acetylglucosamine (O-GlcNAc) modification of proteins provides a mechanism for the control of diverse cellular processes through a dynamic interplay with phosphorylation. UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, UK.

Macromolecule Content

Total Structure Weight: 123.49 kDa
Atom Count: 8,234
Modeled Residue Count: 1,068
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XCOGT	A, B	568	Xanthomonas campestris pv. campestris str. 8004	Mutation(s): 1 EC: 2.4 (PDB Primary Data), 2.4.1.255 (UniProt)
UniProt
Find proteins for A0A0H2XAK3 (Xanthomonas campestris pv. campestris (strain 8004)) Explore A0A0H2XAK3 Go to UniProtKB: A0A0H2XAK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2XAK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.265 (Depositor), 0.264 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.691	α = 90
b = 105.692	β = 90
c = 151.036	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-10
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other