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Protein

Synaptobrevin homolog YKT6

Gene

Ykt6

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Vesicular soluble NSF attachment protein receptor (v-SNARE) mediating vesicle docking and fusion to a specific acceptor cellular compartment. Functions in endoplasmic reticulum to Golgi transport; as part of a SNARE complex composed of GOSR1, GOSR2 and STX5. Functions in early/recycling endosome to TGN transport; as part of a SNARE complex composed of BET1L, GOSR1 and STX5. Has a S-palmitoyl transferase activity.1 Publication

GO - Molecular functioni

  • protein-cysteine S-palmitoyltransferase activity Source: HGNC
  • SNAP receptor activity Source: GO_Central
  • SNARE binding Source: GO_Central

GO - Biological processi

  • ER to Golgi vesicle-mediated transport Source: HGNC
  • exocytosis Source: GO_Central
  • protein transport Source: UniProtKB-KW
  • retrograde transport, endosome to Golgi Source: Ensembl
  • vesicle docking involved in exocytosis Source: HGNC
  • vesicle fusion Source: GO_Central
  • vesicle targeting Source: HGNC
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

ER-Golgi transport, Protein transport, Transport

Enzyme and pathway databases

ReactomeiR-RNO-6807878. COPI-mediated anterograde transport.
R-RNO-6811438. Intra-Golgi traffic.

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptobrevin homolog YKT6 (EC:2.3.1.-)
Gene namesi
Name:Ykt6
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 14

Organism-specific databases

RGDi70897. Ykt6.

Subcellular locationi

GO - Cellular componenti

  • apical dendrite Source: RGD
  • basilar dendrite Source: RGD
  • cytoplasm Source: RGD
  • cytoplasmic vesicle membrane Source: UniProtKB-SubCell
  • cytosol Source: UniProtKB-SubCell
  • endoplasmic reticulum Source: HGNC
  • endosome Source: Ensembl
  • extracellular exosome Source: Ensembl
  • Golgi membrane Source: UniProtKB-SubCell
  • integral component of plasma membrane Source: HGNC
  • membrane Source: RGD
  • mitochondrion Source: Ensembl
  • neuronal cell body Source: RGD
  • SNARE complex Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoplasmic vesicle, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi8 – 81V → D: Mistargeted to Golgi and plasma membrane. Normally targeted to vesicular structures; when associated with A-194 or A-195. 1 Publication
Mutagenesisi39 – 391F → E: Mistargeted to Golgi and plasma membrane; when associated with E-42. Normally targeted to vesicular structures; when associated with E-42 and A-195. 1 Publication
Mutagenesisi42 – 421F → E: Mistargeted to Golgi and plasma membrane; when associated with E-39. Normally targeted to vesicular structures; when associated with E-39 and A-195. 1 Publication
Mutagenesisi50 – 501R → E: Mistargeted to Golgi and plasma membrane; when associated with E-56. Normally targeted to vesicular structures; when associated with E-56 and A-195. 1 Publication
Mutagenesisi56 – 561R → E: Mistargeted to Golgi and plasma membrane; when associated with E-50. Normally targeted to vesicular structures; when associated with E-50 and A-195. 1 Publication
Mutagenesisi59 – 591V → E: Mistargeted to Golgi and plasma membrane. 1 Publication
Mutagenesisi194 – 1941C → A: Loss of prenylation and normally targeted to vesicular structures; when associated with A-195. Normally targeted to vesicular structures; when associated with D-8. 1 Publication
Mutagenesisi195 – 1951C → A: Loss of prenylation and normally targeted to vesicular structures; when associated with A-194. Normally targeted to vesicular structures; when associated with D-8. Normally targeted to vesicular structures; when associated with E-39 and E-42. Normally targeted to vesicular structures; when associated with E-50 and E-56. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 195195Synaptobrevin homolog YKT6PRO_0000280711Add
BLAST
Propeptidei196 – 1983Removed in mature formBy similarityPRO_0000396663

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei159 – 1591PhosphoserineBy similarity
Lipidationi194 – 1941S-palmitoyl cysteineBy similarity
Modified residuei195 – 1951Cysteine methyl esterBy similarity
Lipidationi195 – 1951S-farnesyl cysteineBy similarity

Post-translational modificationi

Palmitoylated; catalyzes its own palmitoylation. Palmitoylation is required for Golgi targeting (By similarity).By similarity
Farnesylation is required for Golgi targeting.

Keywords - PTMi

Lipoprotein, Methylation, Palmitate, Phosphoprotein, Prenylation

Proteomic databases

PaxDbiQ5EGY4.
PRIDEiQ5EGY4.

Expressioni

Tissue specificityi

Highly expressed by neurons in brain and faintly detected in spleen, lung and kidney (at protein level). Ubiquitously expressed.1 Publication

Gene expression databases

GenevisibleiQ5EGY4. RN.

Interactioni

Subunit structurei

Identified in 2 different SNARE complexes; the first one composed of GOSR1, GOSR2 and STX5 and the second one composed of BET1L, GOSR1 and STX5.

GO - Molecular functioni

Protein-protein interaction databases

IntActiQ5EGY4. 6 interactions.
MINTiMINT-4566626.
STRINGi10116.ENSRNOP00000020693.

Structurei

Secondary structure

1
198
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Beta strandi16 – 238Combined sources
Turni30 – 323Combined sources
Helixi33 – 4917Combined sources
Beta strandi55 – 606Combined sources
Beta strandi62 – 709Combined sources
Beta strandi74 – 829Combined sources
Helixi87 – 10418Combined sources
Helixi107 – 1093Combined sources
Turni115 – 1173Combined sources
Helixi123 – 1297Combined sources
Helixi133 – 1353Combined sources
Helixi140 – 1478Combined sources
Beta strandi152 – 1565Combined sources
Helixi157 – 1593Combined sources
Helixi167 – 1737Combined sources
Beta strandi175 – 1773Combined sources
Helixi179 – 19113Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3KYQX-ray2.44A1-198[»]
ProteinModelPortaliQ5EGY4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5EGY4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini8 – 131124LonginPROSITE-ProRule annotationAdd
BLAST
Domaini138 – 19861v-SNARE coiled-coil homologyPROSITE-ProRule annotationAdd
BLAST

Domaini

The longin domain regulates palmitoylation and membrane targeting.By similarity

Sequence similaritiesi

Belongs to the synaptobrevin family.Curated
Contains 1 longin domain.PROSITE-ProRule annotation
Contains 1 v-SNARE coiled-coil homology domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0861. Eukaryota.
COG5143. LUCA.
GeneTreeiENSGT00390000015164.
HOGENOMiHOG000189970.
HOVERGENiHBG088939.
InParanoidiQ5EGY4.
KOiK08516.
OMAiNSCCEIM.
OrthoDBiEOG70KGQV.
PhylomeDBiQ5EGY4.
TreeFamiTF105606.

Family and domain databases

Gene3Di3.30.450.50. 1 hit.
InterProiIPR011012. Longin-like_dom.
IPR010908. Longin_dom.
IPR001388. Synaptobrevin.
[Graphical view]
PfamiPF13774. Longin. 1 hit.
PF00957. Synaptobrevin. 1 hit.
[Graphical view]
SMARTiSM01270. Longin. 1 hit.
[Graphical view]
SUPFAMiSSF64356. SSF64356. 1 hit.
PROSITEiPS50859. LONGIN. 1 hit.
PS50892. V_SNARE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q5EGY4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLYSLSVFY KGEPKAVLLK AAYDVSSFSF FQRSSVQEFM TFTSQLIVER
60 70 80 90 100
SAKGSRASVK EQEYLCHVYV RSDSLAGVVI ADSEYPSRVA FTLLEKVLDE
110 120 130 140 150
FSKQVDRIDW PVGSPATIHY TALDGHLSRY QNPREADPMS KVQAELDETK
160 170 180 190
IILHNTMESL LERGEKLDDL VSKSEVLGTQ SKAFYKTARK QNSCCAIM
Length:198
Mass (Da):22,369
Last modified:March 15, 2005 - v1
Checksum:i384F4EDBC8295407
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti9 – 91F → L in AAD09152 (PubMed:10073573).Curated
Sequence conflicti14 – 141P → K in AAD09152 (PubMed:10073573).Curated
Sequence conflicti100 – 1001E → Q in AAD09152 (PubMed:10073573).Curated
Sequence conflicti107 – 1071R → T in AAD09152 (PubMed:10073573).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF033027 mRNA. Translation: AAD09152.1.
AY881621 mRNA. Translation: AAW81771.1.
RefSeqiNP_113880.2. NM_031692.2.
UniGeneiRn.6525.

Genome annotation databases

EnsembliENSRNOT00000020693; ENSRNOP00000020693; ENSRNOG00000014785.
GeneIDi64351.
KEGGirno:64351.
UCSCiRGD:70897. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF033027 mRNA. Translation: AAD09152.1.
AY881621 mRNA. Translation: AAW81771.1.
RefSeqiNP_113880.2. NM_031692.2.
UniGeneiRn.6525.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3KYQX-ray2.44A1-198[»]
ProteinModelPortaliQ5EGY4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ5EGY4. 6 interactions.
MINTiMINT-4566626.
STRINGi10116.ENSRNOP00000020693.

Proteomic databases

PaxDbiQ5EGY4.
PRIDEiQ5EGY4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000020693; ENSRNOP00000020693; ENSRNOG00000014785.
GeneIDi64351.
KEGGirno:64351.
UCSCiRGD:70897. rat.

Organism-specific databases

CTDi10652.
RGDi70897. Ykt6.

Phylogenomic databases

eggNOGiKOG0861. Eukaryota.
COG5143. LUCA.
GeneTreeiENSGT00390000015164.
HOGENOMiHOG000189970.
HOVERGENiHBG088939.
InParanoidiQ5EGY4.
KOiK08516.
OMAiNSCCEIM.
OrthoDBiEOG70KGQV.
PhylomeDBiQ5EGY4.
TreeFamiTF105606.

Enzyme and pathway databases

ReactomeiR-RNO-6807878. COPI-mediated anterograde transport.
R-RNO-6811438. Intra-Golgi traffic.

Miscellaneous databases

EvolutionaryTraceiQ5EGY4.
PROiQ5EGY4.

Gene expression databases

GenevisibleiQ5EGY4. RN.

Family and domain databases

Gene3Di3.30.450.50. 1 hit.
InterProiIPR011012. Longin-like_dom.
IPR010908. Longin_dom.
IPR001388. Synaptobrevin.
[Graphical view]
PfamiPF13774. Longin. 1 hit.
PF00957. Synaptobrevin. 1 hit.
[Graphical view]
SMARTiSM01270. Longin. 1 hit.
[Graphical view]
SUPFAMiSSF64356. SSF64356. 1 hit.
PROSITEiPS50859. LONGIN. 1 hit.
PS50892. V_SNARE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Characterization of the sequence and expression of a Ykt6 prenylated SNARE from rat."
    Catchpoole D.R., Wanjin H.
    DNA Cell Biol. 18:141-145(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Sprague-Dawley.
    Tissue: Kidney.
  2. "Expression of rat Ykt6 in rat basophil (RBL) cells."
    Lippert U., Ferrari D.M., Jahn R.
    Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Peripheral blood.
  3. "Ykt6 forms a SNARE complex with syntaxin 5, GS28, and Bet1 and participates in a late stage in endoplasmic reticulum-Golgi transport."
    Zhang T., Hong W.
    J. Biol. Chem. 276:27480-27487(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GOSR1; GOSR2 AND STX5.
  4. "Sequential tethering of Golgins and catalysis of SNAREpin assembly by the vesicle-tethering protein p115."
    Shorter J., Beard M.B., Seemann J., Dirac-Svejstrup A.B., Warren G.
    J. Cell Biol. 157:45-62(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH BET1L; GOSR1 AND STX5.
  5. "GS15 forms a SNARE complex with syntaxin 5, GS28, and Ykt6 and is implicated in traffic in the early cisternae of the Golgi apparatus."
    Xu Y., Martin S., James D.E., Hong W.
    Mol. Biol. Cell 13:3493-3507(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH BET1L; GOSR1 AND STX5.
  6. "Mammalian ykt6 is a neuronal SNARE targeted to a specialized compartment by its profilin-like amino terminal domain."
    Hasegawa H., Zinsser S., Rhee Y., Vik-Mo E.O., Davanger S., Hay J.C.
    Mol. Biol. Cell 14:698-720(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, ISOPRENYLATION, SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-194 AND CYS-195.
  7. "Intramolecular protein-protein and protein-lipid interactions control the conformation and subcellular targeting of neuronal Ykt6."
    Hasegawa H., Yang Z., Oltedal L., Davanger S., Hay J.C.
    J. Cell Sci. 117:4495-4508(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF VAL-8; PHE-39; PHE-42; ARG-50; ARG-56 AND VAL-59.

Entry informationi

Entry nameiYKT6_RAT
AccessioniPrimary (citable) accession number: Q5EGY4
Secondary accession number(s): O35487
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: March 15, 2005
Last modified: July 6, 2016
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.