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UniProtKB - Q9H269 (VPS16_HUMAN)

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Protein

Vacuolar protein sorting-associated protein 16 homolog

Gene

VPS16

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

Functioni

Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for recruitment of VPS33A to the HOPS complex (PubMed:23901104). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS33A but not VPS33B (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770).4 Publications3 Publications

GO - Molecular functioni

Complete GO annotation...

GO - Biological processi

  • autophagosome maturation Source: UniProtKB
  • endosome to lysosome transport Source: UniProtKB
  • intracellular protein transport Source: InterPro
  • regulation of SNARE complex assembly Source: GO_Central
  • regulation of vacuole fusion, non-autophagic Source: GO_Central
Complete GO annotation...

Keywordsi

Biological processAutophagy, Protein transport, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 16 homolog
Short name:
hVPS16
Gene namesi
Name:VPS16
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:14584. VPS16.

Subcellular locationi

GO - Cellular componenti

  • autophagosome Source: UniProtKB-SubCell
  • axon Source: Ensembl
  • clathrin-coated vesicle Source: UniProtKB-SubCell
  • early endosome Source: UniProtKB
  • HOPS complex Source: UniProtKB
  • late endosome Source: UniProtKB
  • late endosome membrane Source: UniProtKB-SubCell
  • lysosomal membrane Source: UniProtKB
  • lysosome Source: UniProtKB
  • neuronal cell body Source: Ensembl
  • recycling endosome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasmic vesicle, Endosome, Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

VSP16 mutation have been found in one familly with adolescent-onset primary dystonia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi669A → D: Disrupts interaction with VPS33A, no effect on interaction with VPS18 and impairs endosome-lysosome fusion; when associated with E-725. 2 Publications1
Mutagenesisi725R → E: Disrupts interaction with VPS33A, no effect on interaction with VPS18 and impairs endosome-lysosome fusion; when associated with D-669. 2 Publications1

Keywords - Diseasei

Disease mutation

Organism-specific databases

PharmGKBiPA37903.

Polymorphism and mutation databases

DMDMi23396927.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000658881 – 839Vacuolar protein sorting-associated protein 16 homologAdd BLAST839

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei4Nitrated tyrosineBy similarity1

Keywords - PTMi

Nitration

Proteomic databases

EPDiQ9H269.
MaxQBiQ9H269.
PaxDbiQ9H269.
PeptideAtlasiQ9H269.
PRIDEiQ9H269.

PTM databases

iPTMnetiQ9H269.
PhosphoSitePlusiQ9H269.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000215305.
ExpressionAtlasiQ9H269. baseline and differential.
GenevisibleiQ9H269. HS.

Organism-specific databases

HPAiHPA043229.
HPA048661.

Interactioni

Subunit structurei

Core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, which in HOPS further associates with VPS39 and VPS41 and in CORVET with VPS8 and TGFBRAP1 (PubMed:11382755, PubMed:25783203, PubMed:23901104, PubMed:25266290). Interacts with RAB5C (By similarity). Interacts with STX17, MON1B (PubMed:20434987, PubMed:24554770). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).By similarity2 Publications4 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

Complete GO annotation...

Protein-protein interaction databases

BioGridi122220. 49 interactors.
IntActiQ9H269. 30 interactors.
STRINGi9606.ENSP00000369810.

Structurei

Secondary structure

1839
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi645 – 660Combined sources16
Helixi664 – 687Combined sources24
Helixi696 – 705Combined sources10
Helixi709 – 718Combined sources10
Helixi723 – 734Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BX9X-ray2.60C642-736[»]
ProteinModelPortaliQ9H269.
SMRiQ9H269.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni642 – 736Interaction with VPS33A1 PublicationAdd BLAST95

Sequence similaritiesi

Belongs to the VPS16 family.Curated

Phylogenomic databases

eggNOGiKOG2280. Eukaryota.
ENOG410XQ8X. LUCA.
GeneTreeiENSGT00390000003896.
HOVERGENiHBG056306.
InParanoidiQ9H269.
KOiK20180.
OMAiIRDYHIG.
OrthoDBiEOG091G01XD.
PhylomeDBiQ9H269.
TreeFamiTF105673.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiView protein in InterPro
IPR016534. VPS16.
IPR006925. Vps16_C.
IPR006926. Vps16_N.
IPR015943. WD40/YVTN_repeat-like_dom.
PfamiView protein in Pfam
PF04840. Vps16_C. 1 hit.
PF04841. Vps16_N. 1 hit.
PIRSFiPIRSF007949. VPS16. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H269-1) [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
MDCYTANWNP LGDSAFYRKY ELYSMDWDLK EELRDCLVAA APYGGPIALL 
        60         70         80         90        100
RNPWRKEKAA SVRPVLDIYS ASGMPLASLL WKSGPVVSLG WSAEEELLCV 
       110        120        130        140        150
QEDGAVLVYG LHGDFRRHFS MGNEVLQNRV LDARIFHTEF GSGVAILTGA 
       160        170        180        190        200
HRFTLSANVG DLKLRRMPEV PGLQSAPSCW TVLCQDRVAH ILLAVGPDLY 
       210        220        230        240        250
LLDHAACSAV TPPGLAPGVS SFLQMAVSFT YRHLALFTDT GYIWMGTASL 
       260        270        280        290        300
KEKLCEFNCN IRAPPKQMVW CSRPRSKERA VVVAWERRLM VVGDAPESIQ 
       310        320        330        340        350
FVLDEDSYLV PELDGVRIFS RSTHEFLHEV PAASEEIFKI ASMAPGALLL 
       360        370        380        390        400
EAQKEYEKES QKADEYLREI QELGQLTQAV QQCIEAAGHE HQPDMQKSLL 
       410        420        430        440        450
RAASFGKCFL DRFPPDSFVH MCQDLRVLNA VRDYHIGIPL TYSQYKQLTI 
       460        470        480        490        500
QVLLDRLVLR RLYPLAIQIC EYLRLPEVQG VSRILAHWAC YKVQQKDVSD 
       510        520        530        540        550
EDVARAINQK LGDTPGVSYS DIAARAYGCG RTELAIKLLE YEPRSGEQVP 
       560        570        580        590        600
LLLKMKRSKL ALSKAIESGD TDLVFTVLLH LKNELNRGDF FMTLRNQPMA 
       610        620        630        640        650
LSLYRQFCKH QELETLKDLY NQDDNHQELG SFHIRASYAA EERIEGRVAA 
       660        670        680        690        700
LQTAADAFYK AKNEFAAKAT EDQMRLLRLQ RRLEDELGGQ FLDLSLHDTV 
       710        720        730        740        750
TTLILGGHNK RAEQLARDFR IPDKRLWWLK LTALADLEDW EELEKFSKSK 
       760        770        780        790        800
KSPIGYLPFV EICMKQHNKY EAKKYASRVG PEQKVKALLL VGDVAQAADV 
       810        820        830 
AIEHRNEAEL SLVLSHCTGA TDGATADKIQ RARAQAQKK
Length:839
Mass (Da):94,694
Last modified:September 19, 2002 - v2
Checksum:i9C4292D455C19A60
GO
Isoform 2 (identifier: Q9H269-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     300-443: Missing.

Note: No experimental confirmation available.
Show »
Length:695
Mass (Da):78,300
Checksum:i13D27C230E5CFFCD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti87V → A in BAB71013 (PubMed:14702039).Curated1
Sequence conflicti612E → G in BAB71013 (PubMed:14702039).Curated1
Sequence conflicti690 – 691QF → LQ in AAH12422 (PubMed:15489334).Curated2
Sequence conflicti768N → T in AAG34678 (PubMed:11250079).Curated1
Sequence conflicti809E → D in AAH12422 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07652052N → K Probable disease associated mutation found in patients with adolescent-onset primary dystonia. 1 PublicationCorresponds to variant dbSNP:rs367642720Ensembl.1
Natural variantiVAR_053776637S → I. Corresponds to variant dbSNP:rs35773586Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_004018300 – 443Missing in isoform 2. 1 PublicationAdd BLAST144

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF308801 mRNA. Translation: AAG34678.1.
AK055787 mRNA. Translation: BAB71013.1.
AL161656 Genomic DNA. Translation: CAC21465.1.
AL161656 Genomic DNA. Translation: CAI12120.1.
AL834401 mRNA. Translation: CAD39063.1.
BC012422 mRNA. Translation: AAH12422.1.
BC021291 mRNA. Translation: AAH21291.2.
BC064406 mRNA. Translation: AAH64406.1.
CCDSiCCDS13036.1. [Q9H269-1]
CCDS13037.1. [Q9H269-2]
RefSeqiNP_072097.2. NM_022575.3. [Q9H269-1]
NP_536338.1. NM_080413.2. [Q9H269-2]
UniGeneiHs.269577.

Genome annotation databases

EnsembliENST00000380445; ENSP00000369810; ENSG00000215305. [Q9H269-1]
ENST00000380469; ENSP00000369836; ENSG00000215305. [Q9H269-2]
GeneIDi64601.
KEGGihsa:64601.
UCSCiuc002whe.5. human. [Q9H269-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF308801 mRNA. Translation: AAG34678.1.
AK055787 mRNA. Translation: BAB71013.1.
AL161656 Genomic DNA. Translation: CAC21465.1.
AL161656 Genomic DNA. Translation: CAI12120.1.
AL834401 mRNA. Translation: CAD39063.1.
BC012422 mRNA. Translation: AAH12422.1.
BC021291 mRNA. Translation: AAH21291.2.
BC064406 mRNA. Translation: AAH64406.1.
CCDSiCCDS13036.1. [Q9H269-1]
CCDS13037.1. [Q9H269-2]
RefSeqiNP_072097.2. NM_022575.3. [Q9H269-1]
NP_536338.1. NM_080413.2. [Q9H269-2]
UniGeneiHs.269577.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BX9X-ray2.60C642-736[»]
ProteinModelPortaliQ9H269.
SMRiQ9H269.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122220. 49 interactors.
IntActiQ9H269. 30 interactors.
STRINGi9606.ENSP00000369810.

PTM databases

iPTMnetiQ9H269.
PhosphoSitePlusiQ9H269.

Polymorphism and mutation databases

DMDMi23396927.

Proteomic databases

EPDiQ9H269.
MaxQBiQ9H269.
PaxDbiQ9H269.
PeptideAtlasiQ9H269.
PRIDEiQ9H269.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000380445; ENSP00000369810; ENSG00000215305. [Q9H269-1]
ENST00000380469; ENSP00000369836; ENSG00000215305. [Q9H269-2]
GeneIDi64601.
KEGGihsa:64601.
UCSCiuc002whe.5. human. [Q9H269-1]

Organism-specific databases

CTDi64601.
GeneCardsiVPS16.
H-InvDBiHIX0213048.
HGNCiHGNC:14584. VPS16.
HPAiHPA043229.
HPA048661.
MIMi608550. gene.
neXtProtiNX_Q9H269.
PharmGKBiPA37903.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2280. Eukaryota.
ENOG410XQ8X. LUCA.
GeneTreeiENSGT00390000003896.
HOVERGENiHBG056306.
InParanoidiQ9H269.
KOiK20180.
OMAiIRDYHIG.
OrthoDBiEOG091G01XD.
PhylomeDBiQ9H269.
TreeFamiTF105673.

Miscellaneous databases

ChiTaRSiVPS16. human.
GenomeRNAii64601.
PROiPR:Q9H269.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000215305.
ExpressionAtlasiQ9H269. baseline and differential.
GenevisibleiQ9H269. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiView protein in InterPro
IPR016534. VPS16.
IPR006925. Vps16_C.
IPR006926. Vps16_N.
IPR015943. WD40/YVTN_repeat-like_dom.
PfamiView protein in Pfam
PF04840. Vps16_C. 1 hit.
PF04841. Vps16_N. 1 hit.
PIRSFiPIRSF007949. VPS16. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiVPS16_HUMAN
AccessioniPrimary (citable) accession number: Q9H269
Secondary accession number(s): Q5JUB1
, Q8WU31, Q96EE7, Q96N92, Q9H1Q4, Q9H1Q5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: September 19, 2002
Last modified: May 10, 2017
This is version 140 of the entry and version 2 of the sequence. See 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 20
    Human chromosome 20: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.