VPS50_RAT
ID VPS50_RAT Reviewed; 964 AA.
AC F1LSG8;
DT 24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 62.
DE RecName: Full=Syndetin {ECO:0000250|UniProtKB:Q96JG6};
DE AltName: Full=Coiled-coil domain-containing protein 132 {ECO:0000305};
DE AltName: Full=EARP/GARPII complex subunit VPS50 {ECO:0000312|RGD:1304751};
GN Name=Vps50 {ECO:0000312|RGD:1304751};
GN Synonyms=Ccdc132 {ECO:0000312|RGD:1304751};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15; SER-494; SER-498; SER-559
RP AND SER-561, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
RN [3]
RP SUBCELLULAR LOCATION.
RX PubMed=25799061; DOI=10.1038/ncb3129;
RA Schindler C., Chen Y., Pu J., Guo X., Bonifacino J.S.;
RT "EARP is a multisubunit tethering complex involved in endocytic
RT recycling.";
RL Nat. Cell Biol. 17:639-650(2015).
RN [4]
RP INTERACTION WITH EIPR1.
RX PubMed=27191843; DOI=10.1371/journal.pgen.1006074;
RA Topalidou I., Cattin-Ortola J., Pappas A.L., Cooper K., Merrihew G.E.,
RA MacCoss M.J., Ailion M.;
RT "The EARP complex and its interactor eipr-1 are required for cargo sorting
RT to dense-core vesicles.";
RL PLoS Genet. 12:E1006074-E1006074(2016).
RN [5]
RP INTERACTION WITH EIPR1, AND TISSUE SPECIFICITY.
RX PubMed=27440922; DOI=10.1091/mbc.e16-04-0209;
RA Gershlick D.C., Schindler C., Chen Y., Bonifacino J.S.;
RT "TSSC1 is novel component of the endosomal retrieval machinery.";
RL Mol. Biol. Cell 27:2867-2878(2016).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=31721635; DOI=10.1091/mbc.e18-07-0469;
RA Topalidou I., Cattin-Ortola J., Hummer B., Asensio C.S., Ailion M.;
RT "EIPR1 controls dense-core vesicle cargo retention and EARP complex
RT localization in insulin-secreting cells.";
RL Mol. Biol. Cell 31:59-79(2020).
CC -!- FUNCTION: Acts as component of the EARP complex that is involved in
CC endocytic recycling. The EARP complex associates with Rab4-positive
CC endosomes and promotes recycling of internalized transferrin receptor
CC (TFRC) to the plasma membrane. Within the EARP complex, required to
CC tether the complex to recycling endosomes. Not involved in retrograde
CC transport from early and late endosomes to the trans-Golgi network
CC (TGN). {ECO:0000250|UniProtKB:Q96JG6}.
CC -!- SUBUNIT: Component of the endosome-associated retrograde protein (EARP)
CC complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (By
CC similarity). The EARP complex interacts with EIPR1 (PubMed:27191843,
CC PubMed:27440922). Interacts with VPS51 and VPS53 in an EIPR1-
CC independent manner (By similarity). {ECO:0000250|UniProtKB:Q96JG6,
CC ECO:0000269|PubMed:27191843, ECO:0000269|PubMed:27440922}.
CC -!- SUBCELLULAR LOCATION: Recycling endosome {ECO:0000269|PubMed:25799061}.
CC Membrane {ECO:0000269|PubMed:31721635}. Note=Associates with membranes
CC in an EIPR1-dependent manner. {ECO:0000269|PubMed:31721635}.
CC -!- TISSUE SPECIFICITY: Expressed in the brain (at protein level).
CC {ECO:0000269|PubMed:27440922}.
CC -!- SIMILARITY: Belongs to the syndetin family. {ECO:0000305}.
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DR EMBL; AABR06029416; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR06029417; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR06029418; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001166982.1; NM_001173511.1.
DR AlphaFoldDB; F1LSG8; -.
DR SMR; F1LSG8; -.
DR DIP; DIP-61632N; -.
DR IntAct; F1LSG8; 3.
DR STRING; 10116.ENSRNOP00000059003; -.
DR iPTMnet; F1LSG8; -.
DR jPOST; F1LSG8; -.
DR PaxDb; F1LSG8; -.
DR PRIDE; F1LSG8; -.
DR Ensembl; ENSRNOT00000067087; ENSRNOP00000059003; ENSRNOG00000009894.
DR GeneID; 312083; -.
DR KEGG; rno:312083; -.
DR CTD; 55610; -.
DR RGD; 1304751; Vps50.
DR eggNOG; KOG2939; Eukaryota.
DR GeneTree; ENSGT00390000003442; -.
DR HOGENOM; CLU_009513_1_0_1; -.
DR InParanoid; F1LSG8; -.
DR OMA; MAKVKWD; -.
DR OrthoDB; 293145at2759; -.
DR PRO; PR:F1LSG8; -.
DR Proteomes; UP000002494; Chromosome 4.
DR Bgee; ENSRNOG00000009894; Expressed in quadriceps femoris and 19 other tissues.
DR Genevisible; F1LSG8; RN.
DR GO; GO:1990745; C:EARP complex; ISS:UniProtKB.
DR GO; GO:0016020; C:membrane; IDA:UniProtKB.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
DR GO; GO:0055037; C:recycling endosome; IDA:MGI.
DR GO; GO:0000149; F:SNARE binding; ISO:RGD.
DR GO; GO:0032456; P:endocytic recycling; ISS:UniProtKB.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR InterPro; IPR019514; Syndetin_C.
DR InterPro; IPR040047; VPS50.
DR InterPro; IPR019515; VPS54_N.
DR PANTHER; PTHR13258; PTHR13258; 1.
DR Pfam; PF10474; DUF2451; 1.
DR Pfam; PF10475; Vps54_N; 1.
PE 1: Evidence at protein level;
KW Acetylation; Coiled coil; Endosome; Isopeptide bond; Membrane;
KW Phosphoprotein; Protein transport; Reference proteome; Transport;
KW Ubl conjugation.
FT CHAIN 1..964
FT /note="Syndetin"
FT /id="PRO_0000433424"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 532..563
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 81..107
FT /evidence="ECO:0000255"
FT COILED 216..244
FT /evidence="ECO:0000255"
FT COMPBIAS 1..16
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 549..563
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:Q96JG6"
FT MOD_RES 15
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 494
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 498
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 559
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 561
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CROSSLNK 963
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO1); alternate"
FT /evidence="ECO:0000250|UniProtKB:Q96JG6"
FT CROSSLNK 963
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2); alternate"
FT /evidence="ECO:0000250|UniProtKB:Q96JG6"
SQ SEQUENCE 964 AA; 111188 MW; 517EE3710C8FB162 CRC64;
MQKIKSLMTR QGLKSPPESL NDLGAFESLR VPGKEEFREL REQPSDPQAE QELINSIEQV
YFSADPFDIV KYELEKLPPV LNLQELEEYR DKLKQQQAAV SKKVADLILE KQPAYVKELE
RVTSLQTGLQ LAAVICTNSR RHLNIAKEGF TQASLGLLAN QRKRQLLIGL LKSLRTIKTL
QRTDVRLSEM LEEEDYPGAI QLCLECQKAA STFKHYSCIS ELNSKLQDTL EQIEEQLDVA
LSKICKNFDV NHYTKVQQAY RLLGKTQTAM DQLHMHFTQA IHNTVFQVVL GYVELCAGNT
DTKFQKLQYK DLCTHVTPDS YIPCLADLCK ALWEVMLSYY RTMEWHEKHD SEETAAASEG
SNVMSTEETN FDRGYVKKKL EHGLTRIWQD VQLKVKTYLL GTDLSIFKYD DFIFVLDIVS
RLMQVGEEFC GSKSEVLQES IRKQSINYFK NHHRIRLDEL RMFLENETWE LCPVKSNFSI
LQLHEFKFLE QSRSPSVSPS KQPSATSSKP VTLFEQYCSG GNPFEIQADH KDEETEDVLA
SNGYESDEQE KSAYQDYDSD SDVPEELKRD YVDEQTGDVP VKSVSRETLK SRKKSDYSLN
KVNAPILTNT TLNVIRLVGK YMQMMNILKP IAFDVIHFMS QLFDYYLYAI YTFFGRNDSL
ESTGLGLSSS RLRTTLNRIQ ESLIDLEGSA DPTATLTAAE ERKEKVPSPH LNQLVILTSG
DTLYGLAERV VATESLVFLA EQFEFLQPHL DAVMPAVKKP FLQQFYSQTV STASELRKPI
YWIVAGKAID YEQMLLLMTN VKWDVKEIMS QHNVYVDALL KEFEQFNKRL NEVSKRVRIP
LPVSNILWEH CIRLANRTIV EGYANVKKCS NEGRALMQLD FQQFLMKLEK LTDIRPIPDK
EFVEIYIKAY YLTENDMERW IKEHREYSTK QLTNLVNVCL GSHINKKARQ KLLAAIDDID
RPKR
