Reviewed, UniProtKB/Swiss-Prot Q5VIR6 (VPS53_HUMAN)

Names and origin

Protein names

Recommended name:
    Vacuolar protein sorting-associated protein 53 homolog

Gene names

Name:	VPS53
ORF Names:	PP13624

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	699 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	May be involved in retrograde transport of early and late endosomes to the late Golgi.
Subunit structure	Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS52, VPS53 and VPS54.
Subcellular location	Golgi apparatus › trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein.
Sequence similarities	Belongs to the VPS53 family.
Sequence caution	The sequence AAL55842.1 differs from that shown. Reason: Frameshift at position 562.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Endosome Golgi apparatus Membrane
Coding sequence diversity	Alternative splicing
Domain	Coiled coil
Gene Ontology (GO)
Biological process	protein transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	Golgi apparatus Inferred from electronic annotation. Source: UniProtKB-KW endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q5VIR6-1)

Also known as: long;

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.

Isoform 2 (identifier: Q5VIR6-2)

Also known as: short;

The sequence of this isoform differs from the canonical sequence as follows:
     96-124: Missing.

Isoform 3 (identifier: Q5VIR6-3)

The sequence of this isoform differs from the canonical sequence as follows:
     656-673: LASTRKYFTQFCVKFANS → PVASTRKYFTQLCVKFAK
     674-699: Missing.

Notes: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 699	699	Vacuolar protein sorting-associated protein 53 homolog		PRO_0000215189
Regions
	Coiled coil	55 – 142	88	Potential
Natural variations
	Alternative sequence	96 – 124	29	Missing in isoform 2.		VSP_016236
	Alternative sequence	656 – 673	18	LASTR…KFANS → PVASTRKYFTQLCVKFAK in isoform 3.		VSP_016237
	Alternative sequence	674 – 699	26	Missing in isoform 3.		VSP_016238
Experimental info
	Sequence conflict	466	1	A → T in AAK27973. Ref.2
	Sequence conflict	520	1	T → P in AAK27973. Ref.2
	Sequence conflict	525	1	G → E in AAK27973. Ref.2
	Sequence conflict	658 – 665	8	STRKYFTQ → NMAKSHLY Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (long) [UniParc]. Last modified December 7, 2004. Version 1. Checksum: 6C07EC07682BF4C6	FASTA	699	79,653
	10 20 30 40 50 60 MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT LFPTEQSLAN 70 80 90 100 110 120 IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA QKAIQQLFGK IKDIKDKAEK 130 140 150 160 170 180 SEQMVKEITR DIKQLDHAKR HLTTSITTLN HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG 190 200 210 220 230 240 VMNVLEHFHK YMGIPQIRQL SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD 250 260 270 280 290 300 ACLVANILDP RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE 310 320 330 340 350 360 KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR TTNFEGFLAK 370 380 390 400 410 420 RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE KGDLDQPKKP KAPDNPFHGI 430 440 450 460 470 480 VSKCFEPHLY VYIESQDKNL GELIDRFVAD FKAQGPPKPN TDEGGAVLPS CADLFVYYKK 490 500 510 520 530 540 CMVQCSQLST GEPMIALTTI FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE 550 560 570 580 590 600 VAKFTLEELC LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS 610 620 630 640 650 660 SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP IIRDNLASTR 670 680 690 KYFTQFCVKF ANSFIPKFIT HLFKCKPISM VGAEQVRWT
	Isoform 2 (short) [UniParc]. Checksum: 8057AAC082136EC7		670	76,352
	10 20 30 40 50 60 MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT LFPTEQSLAN 70 80 90 100 110 120 IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQVKEIT RDIKQLDHAK RHLTTSITTL 130 140 150 160 170 180 NHLHMLAGGV DSLEAMTRRR QYGEVANLLQ GVMNVLEHFH KYMGIPQIRQ LSERVKAAQT 190 200 210 220 230 240 ELGQQILADF EEAFPSQGTK RPGGPSNVLR DACLVANILD PRIKQEIIKK FIKQHLSEYL 250 260 270 280 290 300 VLFQENQDVA WLDKIDRRYA WIKRQLVDYE EKYGRMFPRE WCMAERIAVE FCHVTRAELA 310 320 330 340 350 360 KIMRTRAKEI EVKLLLFAIQ RTTNFEGFLA KRFSGCTLTD GTLKKLESPP PSTNPFLEDE 370 380 390 400 410 420 PTPEMEELAT EKGDLDQPKK PKAPDNPFHG IVSKCFEPHL YVYIESQDKN LGELIDRFVA 430 440 450 460 470 480 DFKAQGPPKP NTDEGGAVLP SCADLFVYYK KCMVQCSQLS TGEPMIALTT IFQKYLREYA 490 500 510 520 530 540 WKILSGNLPK TTTSSGGLTI SSLLKEKEGS EVAKFTLEEL CLICNILSTA EYCLATTQQL 550 560 570 580 590 600 EEKLKEKVDV SLIERINLTG EMDTFSTVIS SSIQLLVQDL DAACDPALTA MSKMQWQNVE 610 620 630 640 650 660 HVGDQSPYVT SVILHIKQNV PIIRDNLAST RKYFTQFCVK FANSFIPKFI THLFKCKPIS 670 MVGAEQVRWT
	Isoform 3 [UniParc]. Checksum: 82C41A7433B5EF79		673	76,569
	10 20 30 40 50 60 MMEEEELEFV EELEAVLQLT PEVQLAIEQV FPSQDPLDRA DFNAVEYINT LFPTEQSLAN 70 80 90 100 110 120 IDEVVNKIRL KIRRLDDNIR TVVRGQTNVG QDGRQALEEA QKAIQQLFGK IKDIKDKAEK 130 140 150 160 170 180 SEQMVKEITR DIKQLDHAKR HLTTSITTLN HLHMLAGGVD SLEAMTRRRQ YGEVANLLQG 190 200 210 220 230 240 VMNVLEHFHK YMGIPQIRQL SERVKAAQTE LGQQILADFE EAFPSQGTKR PGGPSNVLRD 250 260 270 280 290 300 ACLVANILDP RIKQEIIKKF IKQHLSEYLV LFQENQDVAW LDKIDRRYAW IKRQLVDYEE 310 320 330 340 350 360 KYGRMFPREW CMAERIAVEF CHVTRAELAK IMRTRAKEIE VKLLLFAIQR TTNFEGFLAK 370 380 390 400 410 420 RFSGCTLTDG TLKKLESPPP STNPFLEDEP TPEMEELATE KGDLDQPKKP KAPDNPFHGI 430 440 450 460 470 480 VSKCFEPHLY VYIESQDKNL GELIDRFVAD FKAQGPPKPN TDEGGAVLPS CADLFVYYKK 490 500 510 520 530 540 CMVQCSQLST GEPMIALTTI FQKYLREYAW KILSGNLPKT TTSSGGLTIS SLLKEKEGSE 550 560 570 580 590 600 VAKFTLEELC LICNILSTAE YCLATTQQLE EKLKEKVDVS LIERINLTGE MDTFSTVISS 610 620 630 640 650 660 SIQLLVQDLD AACDPALTAM SKMQWQNVEH VGDQSPYVTS VILHIKQNVP IIRDNPVAST 670 RKYFTQLCVK FAK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of the human GARP (Golgi associated retrograde protein) complex." Liewen H., Meinhold-Heerlein I., Oliveira V., Schwarzenbacher R., Luo G., Wadle A., Jung M., Pfreundschuh M., Stenner-Liewen F. Exp. Cell Res. 306:24-34(2005) [PubMed: 15878329] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.
[2]	"The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis." Zhao X., He M., Wan D., Ye Y., He Y., Han L., Guo M., Huang Y., Qin W., Wang M.W., Chong W., Chen J., Zhang L., Yang N., Xu B., Wu M., Zuo L., Gu J. Cancer Lett. 190:221-232(2003) [PubMed: 12565177] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Placenta.
[4]	"Large-scale cDNA transfection screening for genes related to cancer development and progression." Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J. Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed: 15498874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-665 (ISOFORM 1).
[5]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 332-699. Tissue: Placenta.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AY444797 mRNA. Translation: AAS20944.1. AF246287 mRNA. Translation: AAK27973.1. BC006116 mRNA. Translation: AAH06116.1. AF318335 mRNA. Translation: AAL55842.1. Frameshift. AK001841 mRNA. Translation: BAA91935.1.
UniGene	Hs.461819
3D structure databases
ModBase	Search...
PTM databases
PhosphoSite	Q5VIR6.
Genome annotation databases
Ensembl	ENSG00000141252. Homo sapiens. [Contig view]
Organism-specific databases
H-InvDB	HIX0013386.
HGNC	HGNC:25608. VPS53.
PharmGKB	PA142670618.
GenAtlas	Search...
GeneCards	Search...
Phylogenomic databases
HOVERGEN	Q5VIR6.
Gene expression databases
ArrayExpress	Q5VIR6.
CleanEx	HS_VPS53.
GermOnline	ENSG00000141252. Homo sapiens.
Family and domain databases
InterPro	IPR007234. Vps53_N. [Graphical view]
Pfam	PF04100. Vps53_N. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

VPS53_HUMAN

Accession

Primary (citable) accession number: Q5VIR6
Secondary accession number(s): Q8WYW3 , Q9BRR2, Q9BY02, Q9NV25

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	December 7, 2004
Last modified:	November 25, 2008
This is version 40 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)