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Glycosciences.DB structure entry #556: O-GlcNAc linked to Ser

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Format: CarbBank LINUCS GlycoCT_xml


 b-D-GlcpNAc-(1-3)-Ser


<?xml version="1.0" encoding="UTF-8"?>
 <sugar version="1.0">
 <residues>
 <basetype id="1" anomer="b" superclass="hex" ringStart="1" ringEnd="5" name="b-dglc-HEX-1:5">
 <stemtype id="1" type="dglc" />
 </basetype>
 <substituent id="2" name="n-acetyl" />
 </residues>
 <linkages>
 <connection id="1" parent="1" child="2">
 <linkage id="1" parentType="d" childType="n">
 <parent pos="2" />
 <child pos="1" />
 </linkage>
 </connection>
 </linkages>
 <aglyca>
 <historicalData>
 <entry id="0" name="SER" toResidue="1">
 <linkage parentType="n" childType="x">
 <parent pos="3" />
 <child pos="1" />
 </linkage>
 </entry>
 </historicalData>
 </aglyca>
 </sugar>

SNFG-style Graphics

3D Structure Model

download coordinates

Corresponding entries: 48

1 - 5 of 48 entries with matching glycan part

Structure entry #229: N-Glycan fragment GlcNAc1

b-D-GlcpNAc-(1-4)-Asn

NMR spectra

literature references

no GlycoMaps

Structure entry #588:

b-D-GlcpNAc-(1-3)+ | Ser-(1-2)-Ala | Gly-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #594:

b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Gly-(1-2)-Ser-(1-2)-Met-(1-2)-Ser-(1-2)-Gly | Thr-(1-2)-His-(1-2)-Ala-(1-2)-Ser-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #595:

b-D-GlcpNAc-(1-4)+ | Asn-(1-2)-Lys-(1-2)-Thr-(1-2)-Leu-(1-2)-Met | Gly-(1-2)-Lys-(1-2)-Ala-(1-2)-Tyr-(1-2)-Thr-(1-2)-Ile-(1-2)-Phe-(1-2)+

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

Structure entry #2038:

b-D-GlcpNAc-(1-1)-<linker-TMR>

no 3d model

no NMR spectra

literature references

no GlycoMaps

Taxons

O-GlcNAc

General Structure Data

Chemical Formula:	C₁₁H₂₀N₂O₇		#C	#H	#O	#N
Molec. Weight:	292		11	20	7	2
# Atoms:	40
# Residues:	2
# Heavy Atoms:	20

Superclasses:

Hex
HexNAc	1

Residues:

Residue	Count
B-D-GLCPNAC	1
SER	1

PDB references: 27

1 - 5 of 27 PDB entries

PDB ID 7wgb: Neutral Omicron Spike Trimer in complex with ACE2

Description:

Source: Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Experimental method: ELECTRON MICROSCOPY

Release date: 2022-06-22

Entry features 4 distinct glycan structures [41 instances].

PDB ID 7ec3: Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)

Description:

Source: Staphylococcus aureus (strain USA300)

Experimental method: X-RAY DIFFRACTION

Resolution: 2.5Å

Release date: 2022-03-16

Entry features 2 distinct glycan structures [5 instances].

PDB ID 6byj: Structure of human 14-3-3 gamma bound to O-GlcNAc peptide

Description: 14-3-3 protein gamma, TSTTATPPVSQASSTTTSTW O-GlcNac peptide

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.9Å

Release date: 2018-05-09

Entry features 1 distinct glycan structures [3 instances].

PDB ID 6byk: Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide

Description: 14-3-3 protein beta/alpha, ATPPVSQASSTT O-GlcNac peptide

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 3Å

Release date: 2018-05-09

Entry features 1 distinct glycan structures [4 instances].

PDB ID 6bzd: Structure of 14-3-3 gamma R57E mutant bound to GlcNAcylated peptide

Description: 14-3-3 protein gamma, GlcNAcylated peptide

Source: Homo sapiens

Experimental method: X-RAY DIFFRACTION

Resolution: 2.67Å

Release date: 2018-05-09

Entry features 1 distinct glycan structures [2 instances].

Literature references: 73

1 - 5 of 73 literature references

Reference #21958

Schwein PA; Ge Y; Yang B; D'Souza A; Mody A; Shen D; Woo CM

Writing and Erasing O-GlcNAc on Casein Kinase 2 Alpha Alters the Phosphoproteome.

Published 2022 in ACS Chem Biol, : Online ahead of print

Reference contains 2 structures

Reference #22021

Lv P; Du Y; He C; Peng L; Zhou X; Wan Y; Zeng M; Zhou W; Zou P; Li C; Zhang M; Dong S; Chen X

O-GlcNAcylation modulates liquid-liquid phase separation of SynGAP/PSD-95.

Published 2022 in Nat Chem, :

Reference contains 2 structures

Reference #22446

Xu B; Zhang C; Jiang A; Zhang X; Liang F; Wang X; Li D; Liu C; Liu X; Xia J; Li Y; Wang Y; Yang Z; Chen J; Zhou Y; Chen L; Sun H

Histone methyltransferase Dot1L recruits O-GlcNAc transferase to target chromatin sites to regulate histone O-GlcNAcylation.

Published 2022 in J Biol Chem, 298: 102115

Reference contains 2 structures

Reference #22504

Wang Y; Shu H; Liu J; Jin X; Wang L; Qu Y; Xia M; Peng P; Feng Y; Wei M

EGF promotes PKM2 O-GlcNAcylation by stimulating O-GlcNAc transferase phosphorylation at Y976 and their subsequent association.

Published 2022 in J Biol Chem, 298: 102340

Reference contains 2 structures

Reference #21890

King DT; Serrano-Negrón JE; Zhu Y; Moore CL; Shoulders MD; Foster LJ; Vocadlo DJ

Thermal Proteome Profiling Reveals the O-GlcNAc-Dependent Meltome.

Published 2022 in J Am Chem Soc, : epub ahead of print

Reference contains 2 structures

Further literature references from PDB entries: 14

1 - 5 of 14 literature references from PDB entries

Reference #22040

Cui Z; Liu P; Wang N; Wang L; Fan K; Zhu Q; Wang K; Chen R; Feng R; Jia Z; Yang M; Xu G; Zhu B; Fu W; Chu T; Feng L; Wang Y; Pei X; Yang P; Xie XS; Cao L; Cao Y; Wang X

Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron.

Published 2022 in Cell, 185: 860-871.e13

Reference #20278

Rafie K; Raimi O; Ferenbach AT; Borodkin VS; Kapuria V; van Aalten DMF

Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats.

Published 2017 in Open Biol, 7:

Reference #20071

Janetzko J; Trauger SA; Lazarus MB; Walker S

How the glycosyltransferase OGT catalyzes amide bond cleavage.

Published 2016 in Nat. Chem. Biol., 12: 899-901

Reference #19367

Ostrowski A; Gundogdu M; Ferenbach AT; Lebedev AA; van Aalten DM

Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum.

Published 2015 in J. Biol. Chem., 290: 30291-305

Reference #18113

Schimpl M; Borodkin VS; Gray LJ; van Aalten DM

Synergy of peptide and sugar in O-GlcNAcase substrate recognition.

Published 2012 in Chem. Biol., 19: 173-8

NCBI Taxonomy ID	Scientific Name
9606	Homo sapiens
1639	Listeria monocytogenes
40674	Mammalia
1302	Streptococcus gordonii

Consortium for Functional Glycomics (CFG):

GlycoEpitope DB:

EP0004

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