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Protein

Glycogenin-1

Gene

GYG1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.

Catalytic activityi

UDP-alpha-D-glucose + glycogenin = UDP + alpha-D-glucosylglycogenin.

Cofactori

Mn2+Note: Divalent metal ions. Required for self-glucosylation. Manganese is the most effective.

Pathwayi: glycogen biosynthesis

This protein is involved in the pathway glycogen biosynthesis, which is part of Glycan biosynthesis.
View all proteins of this organism that are known to be involved in the pathway glycogen biosynthesis and in Glycan biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei86By similarity1
Metal bindingi102ManganeseBy similarity1
Metal bindingi104ManganeseBy similarity1
Sitei160Important for catalytic activityBy similarity1
Sitei163Important for catalytic activityBy similarity1
Metal bindingi212ManganeseBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Glycogen biosynthesis

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:HS08931-MONOMER.
ZFISH:HS08931-MONOMER.
BRENDAi2.4.1.186. 2681.
ReactomeiR-HSA-3322077. Glycogen synthesis.
R-HSA-3785653. Myoclonic epilepsy of Lafora.
R-HSA-3814836. Glycogen storage disease type XV (GYG1).
R-HSA-3828062. Glycogen storage disease type 0 (muscle GYS1).
R-HSA-3878781. Glycogen storage disease type IV (GBE1).
R-HSA-5357572. Lysosomal glycogen catabolism.
R-HSA-5357609. Glycogen storage disease type II (GAA).
R-HSA-6798695. Neutrophil degranulation.
R-HSA-70221. Glycogen breakdown (glycogenolysis).
UniPathwayiUPA00164.

Protein family/group databases

CAZyiGT8. Glycosyltransferase Family 8.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycogenin-1 (EC:2.4.1.186)
Short name:
GN-1
Short name:
GN1
Gene namesi
Name:GYG1
Synonyms:GYG
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:4699. GYG1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • extracellular exosome Source: UniProtKB
  • lysosomal lumen Source: Reactome
  • membrane Source: UniProtKB
Complete GO annotation...

Pathology & Biotechi

Involvement in diseasei

Glycogen storage disease 15 (GSD15)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA metabolic disorder resulting in muscle weakness, associated with the glycogen depletion in skeletal muscle, and cardiac arrhythmia, associated with the accumulation of abnormal storage material in the heart. The skeletal muscle shows a marked predominance of slow-twitch, oxidative muscle fibers and mitochondrial proliferation.
See also OMIM:613507
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06376883T → M in GSD15; inactivation of the autoglucosylation. 1 PublicationCorresponds to variant rs267606858dbSNPEnsembl.1
Polyglucosan body myopathy 2 (PGBM2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA glycogen storage disease characterized by polyglucosan accumulation in muscle, and skeletal myopathy without cardiac involvement. Most patients manifest slowly progressive, hip girdle, shoulder girdle, and/or hand and leg muscle weakness. Polyglucosan contains abnormally long and poorly branched glucosyl chains and is variably resistant to digestion by alpha-amylase.
See also OMIM:616199
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07270616A → P in PGBM2. 1 Publication1
Natural variantiVAR_072707102D → H in PGBM2. 1 PublicationCorresponds to variant rs143137713dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, Glycogen storage disease

Organism-specific databases

DisGeNETi2992.
MalaCardsiGYG1.
MIMi613507. phenotype.
616199. phenotype.
OpenTargetsiENSG00000163754.
Orphaneti263297. Glycogen storage disease due to glycogenin deficiency.
PharmGKBiPA29077.

Polymorphism and mutation databases

BioMutaiGYG1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002151762 – 350Glycogenin-1CuratedAdd BLAST349

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonineCombined sources1
Modified residuei44PhosphoserineBy similarity1
Glycosylationi195O-linked (Glc...)By similarity1

Post-translational modificationi

Self-glycosylated by the transfer of glucose residues from UDP-glucose to itself, forming an alpha-1,4-glycan of around 10 residues attached to Tyr-195.
Phosphorylated.By similarity

Keywords - PTMi

Acetylation, Glycoprotein, Phosphoprotein

Proteomic databases

EPDiP46976.
MaxQBiP46976.
PaxDbiP46976.
PeptideAtlasiP46976.
PRIDEiP46976.

PTM databases

iPTMnetiP46976.
PhosphoSitePlusiP46976.

Expressioni

Gene expression databases

BgeeiENSG00000163754.
CleanExiHS_GYG1.
ExpressionAtlasiP46976. baseline and differential.
GenevisibleiP46976. HS.

Organism-specific databases

HPAiHPA030497.

Interactioni

Subunit structurei

Homodimer tightly complexed to the 86 kDa catalytic subunit of glycogen synthase GYS1 (By similarity). Interacts (via C-terminus) with GYS2 (PubMed:17055998). This interaction is required for GYS2-mediated glycogen synthesis (By similarity).By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
GYS1P138077EBI-740533,EBI-740553

Protein-protein interaction databases

BioGridi109247. 19 interactors.
IntActiP46976. 14 interactors.
MINTiMINT-5000544.
STRINGi9606.ENSP00000340736.

Structurei

Secondary structure

1350
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 12Combined sources9
Helixi13 – 28Combined sources16
Beta strandi33 – 39Combined sources7
Helixi45 – 54Combined sources10
Beta strandi55 – 60Combined sources6
Helixi69 – 74Combined sources6
Helixi80 – 91Combined sources12
Beta strandi96 – 101Combined sources6
Beta strandi105 – 107Combined sources3
Helixi112 – 116Combined sources5
Beta strandi119 – 124Combined sources6
Beta strandi126 – 128Combined sources3
Beta strandi131 – 139Combined sources9
Helixi143 – 156Combined sources14
Beta strandi159 – 161Combined sources3
Helixi163 – 170Combined sources8
Turni171 – 176Combined sources6
Helixi179 – 181Combined sources3
Helixi185 – 187Combined sources3
Beta strandi188 – 190Combined sources3
Helixi191 – 195Combined sources5
Helixi198 – 204Combined sources7
Helixi205 – 207Combined sources3
Beta strandi209 – 212Combined sources4
Beta strandi215 – 217Combined sources3
Helixi219 – 221Combined sources3
Beta strandi222 – 225Combined sources4
Turni226 – 229Combined sources4
Beta strandi230 – 232Combined sources3
Helixi238 – 240Combined sources3
Helixi244 – 256Combined sources13
Helixi258 – 261Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3Q4SX-ray1.98A1-262[»]
3QVBX-ray2.26A1-262[»]
3RMVX-ray1.82A1-262[»]
3RMWX-ray1.93A1-262[»]
3T7MX-ray1.80A/B1-262[»]
3T7NX-ray1.98A/B1-262[»]
3T7OX-ray1.85A/B1-262[»]
3U2TX-ray2.05A1-262[»]
3U2UX-ray1.45A/B1-262[»]
3U2VX-ray1.50A/B1-262[»]
3U2WX-ray1.68A/B1-262[»]
3U2XX-ray1.77A/B1-262[»]
ProteinModelPortaliP46976.
SMRiP46976.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP46976.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni301 – 333Interaction with GYS11 PublicationAdd BLAST33

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1950. Eukaryota.
COG5597. LUCA.
GeneTreeiENSGT00390000004721.
HOGENOMiHOG000008282.
HOVERGENiHBG000681.
InParanoidiP46976.
KOiK00750.
OMAiSESHDPN.
OrthoDBiEOG091G09E1.
PhylomeDBiP46976.
TreeFamiTF312839.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
InterProiIPR002495. Glyco_trans_8.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01501. Glyco_transf_8. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform GN-1L (identifier: P46976-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTDQAFVTLT TNDAYAKGAL VLGSSLKQHR TTRRLVVLAT PQVSDSMRKV
60 70 80 90 100
LETVFDEVIM VDVLDSGDSA HLTLMKRPEL GVTLTKLHCW SLTQYSKCVF
110 120 130 140 150
MDADTLVLAN IDDLFDREEL SAAPDPGWPD CFNSGVFVYQ PSVETYNQLL
160 170 180 190 200
HLASEQGSFD GGDQGILNTF FSSWATTDIR KHLPFIYNLS SISIYSYLPA
210 220 230 240 250
FKVFGASAKV VHFLGRVKPW NYTYDPKTKS VKSEAHDPNM THPEFLILWW
260 270 280 290 300
NIFTTNVLPL LQQFGLVKDT CSYVNVLSDL VYTLAFSCGF CRKEDVSGAI
310 320 330 340 350
SHLSLGEIPA MAQPFVSSEE RKERWEQGQA DYMGADSFDN IKRKLDTYLQ
Length:350
Mass (Da):39,384
Last modified:January 23, 2007 - v4
Checksum:iABAEEB7160DEC4DF
GO
Isoform GN-1 (identifier: P46976-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     277-293: Missing.

Show »
Length:333
Mass (Da):37,479
Checksum:iCD5E3C16F849FF7C
GO
Isoform GN-1S (identifier: P46976-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     204-350: FGASAKVVHF...IKRKLDTYLQ → KMSQEPYHIC...IHFTSLVSDT

Show »
Length:279
Mass (Da):31,467
Checksum:iF8AD62431CBB470E
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07270616A → P in PGBM2. 1 Publication1
Natural variantiVAR_06376883T → M in GSD15; inactivation of the autoglucosylation. 1 PublicationCorresponds to variant rs267606858dbSNPEnsembl.1
Natural variantiVAR_072707102D → H in PGBM2. 1 PublicationCorresponds to variant rs143137713dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_001768204 – 350FGASA…DTYLQ → KMSQEPYHICPLGRSQLWHS RLYPRKNGRNDGNRARLIIW EQIPLTTSRGNLTLTSSRNT AFFCEHIHFTSLVSDT in isoform GN-1S. CuratedAdd BLAST147
Alternative sequenceiVSP_001769277 – 293Missing in isoform GN-1. 4 PublicationsAdd BLAST17

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44131 mRNA. Translation: AAB00114.1.
U31525 mRNA. Translation: AAB09752.1.
X79537 mRNA. Translation: CAA56073.1.
AF065481
, AF065476, AF065477, AF065478, AF065479, AF065480 Genomic DNA. Translation: AAD31084.1.
AF087942 mRNA. Translation: AAD52093.1.
CR536547 mRNA. Translation: CAG38784.1.
AC021059 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW78894.1.
CH471052 Genomic DNA. Translation: EAW78895.1.
CH471052 Genomic DNA. Translation: EAW78896.1.
CH471052 Genomic DNA. Translation: EAW78898.1.
CH471052 Genomic DNA. Translation: EAW78900.1.
CH471052 Genomic DNA. Translation: EAW78901.1.
BC000033 mRNA. Translation: AAH00033.1.
CCDSiCCDS3139.1. [P46976-1]
CCDS54654.1. [P46976-2]
CCDS54655.1. [P46976-3]
PIRiJC4695.
RefSeqiNP_001171649.1. NM_001184720.1. [P46976-2]
NP_001171650.1. NM_001184721.1. [P46976-3]
NP_004121.2. NM_004130.3. [P46976-1]
UniGeneiHs.477892.

Genome annotation databases

EnsembliENST00000296048; ENSP00000296048; ENSG00000163754. [P46976-2]
ENST00000345003; ENSP00000340736; ENSG00000163754. [P46976-1]
ENST00000484197; ENSP00000420683; ENSG00000163754. [P46976-3]
GeneIDi2992.
KEGGihsa:2992.
UCSCiuc003ewn.4. human. [P46976-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44131 mRNA. Translation: AAB00114.1.
U31525 mRNA. Translation: AAB09752.1.
X79537 mRNA. Translation: CAA56073.1.
AF065481
, AF065476, AF065477, AF065478, AF065479, AF065480 Genomic DNA. Translation: AAD31084.1.
AF087942 mRNA. Translation: AAD52093.1.
CR536547 mRNA. Translation: CAG38784.1.
AC021059 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW78894.1.
CH471052 Genomic DNA. Translation: EAW78895.1.
CH471052 Genomic DNA. Translation: EAW78896.1.
CH471052 Genomic DNA. Translation: EAW78898.1.
CH471052 Genomic DNA. Translation: EAW78900.1.
CH471052 Genomic DNA. Translation: EAW78901.1.
BC000033 mRNA. Translation: AAH00033.1.
CCDSiCCDS3139.1. [P46976-1]
CCDS54654.1. [P46976-2]
CCDS54655.1. [P46976-3]
PIRiJC4695.
RefSeqiNP_001171649.1. NM_001184720.1. [P46976-2]
NP_001171650.1. NM_001184721.1. [P46976-3]
NP_004121.2. NM_004130.3. [P46976-1]
UniGeneiHs.477892.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3Q4SX-ray1.98A1-262[»]
3QVBX-ray2.26A1-262[»]
3RMVX-ray1.82A1-262[»]
3RMWX-ray1.93A1-262[»]
3T7MX-ray1.80A/B1-262[»]
3T7NX-ray1.98A/B1-262[»]
3T7OX-ray1.85A/B1-262[»]
3U2TX-ray2.05A1-262[»]
3U2UX-ray1.45A/B1-262[»]
3U2VX-ray1.50A/B1-262[»]
3U2WX-ray1.68A/B1-262[»]
3U2XX-ray1.77A/B1-262[»]
ProteinModelPortaliP46976.
SMRiP46976.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109247. 19 interactors.
IntActiP46976. 14 interactors.
MINTiMINT-5000544.
STRINGi9606.ENSP00000340736.

Protein family/group databases

CAZyiGT8. Glycosyltransferase Family 8.

PTM databases

iPTMnetiP46976.
PhosphoSitePlusiP46976.

Polymorphism and mutation databases

BioMutaiGYG1.

Proteomic databases

EPDiP46976.
MaxQBiP46976.
PaxDbiP46976.
PeptideAtlasiP46976.
PRIDEiP46976.

Protocols and materials databases

DNASUi2992.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000296048; ENSP00000296048; ENSG00000163754. [P46976-2]
ENST00000345003; ENSP00000340736; ENSG00000163754. [P46976-1]
ENST00000484197; ENSP00000420683; ENSG00000163754. [P46976-3]
GeneIDi2992.
KEGGihsa:2992.
UCSCiuc003ewn.4. human. [P46976-1]

Organism-specific databases

CTDi2992.
DisGeNETi2992.
GeneCardsiGYG1.
HGNCiHGNC:4699. GYG1.
HPAiHPA030497.
MalaCardsiGYG1.
MIMi603942. gene.
613507. phenotype.
616199. phenotype.
neXtProtiNX_P46976.
OpenTargetsiENSG00000163754.
Orphaneti263297. Glycogen storage disease due to glycogenin deficiency.
PharmGKBiPA29077.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1950. Eukaryota.
COG5597. LUCA.
GeneTreeiENSGT00390000004721.
HOGENOMiHOG000008282.
HOVERGENiHBG000681.
InParanoidiP46976.
KOiK00750.
OMAiSESHDPN.
OrthoDBiEOG091G09E1.
PhylomeDBiP46976.
TreeFamiTF312839.

Enzyme and pathway databases

UniPathwayiUPA00164.
BioCyciMetaCyc:HS08931-MONOMER.
ZFISH:HS08931-MONOMER.
BRENDAi2.4.1.186. 2681.
ReactomeiR-HSA-3322077. Glycogen synthesis.
R-HSA-3785653. Myoclonic epilepsy of Lafora.
R-HSA-3814836. Glycogen storage disease type XV (GYG1).
R-HSA-3828062. Glycogen storage disease type 0 (muscle GYS1).
R-HSA-3878781. Glycogen storage disease type IV (GBE1).
R-HSA-5357572. Lysosomal glycogen catabolism.
R-HSA-5357609. Glycogen storage disease type II (GAA).
R-HSA-6798695. Neutrophil degranulation.
R-HSA-70221. Glycogen breakdown (glycogenolysis).

Miscellaneous databases

ChiTaRSiGYG1. human.
EvolutionaryTraceiP46976.
GenomeRNAii2992.
PROiP46976.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000163754.
CleanExiHS_GYG1.
ExpressionAtlasiP46976. baseline and differential.
GenevisibleiP46976. HS.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
InterProiIPR002495. Glyco_trans_8.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01501. Glyco_transf_8. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiGLYG_HUMAN
AccessioniPrimary (citable) accession number: P46976
Secondary accession number(s): D3DNH0
, D3DNH1, D3DNH2, Q6FHZ1, Q9UNV0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 162 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.