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NAPA (N-ethylmaleimide-sensitive factor attachment protein, alpha)

Written2013-09Nayden G Naydenov, Andrei I Ivanov
Department of Human, Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA (NGN); Department of Human, Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA (AII)

(Note : for Links provided by Atlas : click)

Identity

Alias_namesN-ethylmaleimide-sensitive factor attachment protein
Other aliasSNAPA
HGNC (Hugo) NAPA
LocusID (NCBI) 8775
Atlas_Id 44025
Location 19q13.32  [Link to chromosome band 19q13]
Location_base_pair Starts at 47487634 and ends at 47515258 bp from pter ( according to hg19-Feb_2009)  [Mapping NAPA.png]
Local_order The human NAPA gene maps on 19q13 between the ZNF541 (zing finger protein 541) and the KPTN, (kaptin) (actin binding protein) loci.
Fusion genes
(updated 2016)
NAPA (19q13.32) / BCL6 (3q27.3)S100A8 (1q21.3) / NAPA (19q13.32)TTLL5 (14q24.3) / NAPA (19q13.32)
Note No translocations reported.

DNA/RNA

 
  Figure 1. Schematic representation of the genomic structure of human NAPA gene-transcript variant 1, (ENST00000263354). Exons are represented by red boxes while introns appear as waved black lines. The length of exons in (bp) is shown in the red boxes, and that of the introns is presented at the bottom blue boxes (not to scale). The relative position of ATG start and TAA stop codons are indicated with black arrows.
Description The NAPA gene spans 27,61 kb on chromosome 19q13 and consists of 11 exons and 10 introns (fig. 1) with an open reading frame of 1839 bp. The NAPA promoter has not been functionally explored.
Transcription The predominant transcript variant (1) of the NAPA gene encodes a functional protein of 295 amino acids. The second transcript of 1521 bp is predicted to encode a 256 amino acid protein. This variant (2) uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the alternate splice site renders the resulting transcript a candidate for nonsense-mediated mRNA decay (NMD). The third transcript, variant (3), is 1668 bp. Variant (3) lacks two consecutive internal exons, compared to variant 1. This variant is also represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, also makes this transcript a candidate for NMD. Additionally, 2 alternative transcribed variants are predicted to exist via the automatic annotation program, Havana. However, these predicted transcripts need to be experimentally confirmed.
Pseudogene None discovered.

Protein

Description The sequence of the predicted 295-amino acid; 33233 Da human protein encoded by NAPA shares 37%, 60%, and 81% identity with sequences in yeast (Sacharomyces cerevisiae), Drosophila melanogaster, and zebrafish (Danio rerio). NAPA belongs to a protein family comprised of, in higher eukaryotes, three homologues named NAPA, soluble NSF attachment protein beta (NAPB), and soluble NSF attachment protein gamma (NAPG) (Clary et al., 1990). Amino acid sequence comparison of bovine proteins show that NAPA and NAPB are most related to each other with 83% amino acid identity (Whiteheart et al., 1993). In contrast, NAPA and NAPG have only about 25% sequence identity. Structural information is available for the yeast homolog of NAPA, Sec17 (Rice and Brunger, 1999), and zebrafish NAPG (Bitto et al., 2008). Both homologs represent elongated proteins comprised of an extended twisted sheet of α-helical hairpins and a helical-bundle domain at the carboxy-terminal end.
Expression NAPA is ubiquitously expressed in various mammalian cells and tissues. In mouse tissues, its expression level is highest in the brain, spleen, and testis (Whiteheart et al., 1993). Data from the human gene atlas has shown that NAPA is expressed at the highest level in heart, liver, lung, and placenta. Regulation of NAPA expression remains unexplored. One recent report demonstrated decreased protein levels of NAPA in brain synaptosomes of rats subjected to oxidative stress (Kaneai et al., 2013).
Localisation In polarized epithelial cells such as alveolar type II cells, T84, and SK-CO15 human colonic epithelial cells NAPA predominantly localizes in the plasma membrane with significant enrichment at the apical junctional complex (Abonyo et al., 2003; Naydenov et al., 2012a). By contrast, in contact-naïve epithelial cells, NAPA accumulates in the perinuclear intracellular compartment that resembles the Golgi complex (Naydenov et al., 2012a).
 
  Figure 2. A model depicting vesicle fusion events according to the SNARE hypothesis. During the initial docking step, v-SNARE and t-SNARE bind creating a complex that drives pore formation and fusion of the two opposing membranes. After the fusion step, NAPA is recruited to the cys-SNARE complex allowing NSF binding. Next the ATPase activity of NSF and conformational changes of both NSF and NAPA disassemble the cys-SNARE complex, and release its components for recycling in subsequent fusion events.
Function One of the most-studied intracellular functions of NAPA involves regulation of NSF-dependent vesicle fusion (Andreeva et al., 2006). According to the so-called "SNARE (soluble NSF attachment protein receptor) hypothesis" vesicle fusion is driven by specific associations of complementary SNARE proteins residing on the vesicle (v-SNAREs) and target (t-SNAREs) membranes (Chen and Scheller, 2001). These proteins form a core SNARE complex consisting of a parallel four-helix bundle. This complex drives the opposing membranes to a close apposition, and subsequently to a complete fusion (fig. 2). Eukaryotic cells use an evolutionarily-conserved mechanism to disassemble and recycle the cys-SNARE complex that is formed after the fusion of two membranes (Barnard et al., 1997). This mechanism involves a hexameric ATPase, NSF, and its adaptor protein, NAPA (Vivona et al., 2013; Wilson et al., 1992; Winter et al., 2009). NAPA interacts with the SNARE complex, recruits NSF, stimulates NSF activity, and transduces a conformational change of NSF to drive SNARE disassembly (fig. 2). NAPA was implicated in the regulation of numerous trafficking/fusion events in different cellular compartments (Andreeva et al., 2006). Examples of this regulation include ER-Golgi transport, intra-Golgi vesicle fusion, trafficking from the trans-Golgi network to the plasma membrane, neuromediator exocytosis, and synaptic vesicle fusion (Barnard et al., 1997; Burgalossi et al., 2010; Clary et al., 1990; Low et al., 1998; Peter et al., 1998; Xu et al., 2002). Interestingly, recent studies discovered several NSF-independent activities of NAPA. These activities involve assembly of epithelial junctions (Andreeva et al., 2005; Naydenov et al., 2012a), suppression of cell apoptosis (Naydenov et al., 2012b; Wu and Chao, 2010), and autophagy (Naydenov et al., 2012c), as well as regulation of store-operated calcium entry (Miao et al., 2013). Such NSF-independent functions are likely to depend on NAPA interactions with different binding partners. For example, NAPA may suppress apoptosis due to its binding to the ER-resident, pro-apoptotic protein BNIP1 (Nakajima et al., 2004). Furthermore, NAPA-dependent regulation of autophagy can be mediated by its ability to interact and dephosphorylate AMP-activated protein kinase (Wang and Brautigan, 2013).

Mutations

Note A missense G to A transition that leads to a change from methionine to isoleucine (M105I) has been detected in mice (Chae et al., 2004; Hong et al., 2004). This mutation leads to the appearance of the so-called hyh (hydrocephalus with hop gait) phenotype and also impairs acrosomal exocytosis in sperm (Bátiz et al., 2009). Other mutations have not been found associated with this gene potentially because of the multiple roles of NAPA in critical cellular functions which would prevent survival of cells with dysfunctional NAPA mutations.

Implicated in

Note
  
Entity Colorectal cancer
Note A study utilizing patients with small undifferentiated colorectal cancer revealed a significant increase of NAPA immunoreactivity in cancer cells that correlated with a more aggressive course of the disease (Grabowski et al., 2002).
  
  
Entity Down syndrome
Note One study has analyzed expression of NAPA protein in fetal cortex samples of patients with Down Syndrome. The study reported a significant decrease in NAPA expression compared to control samples that correlated with deterioration of the neuronal dendritic tree (Weitzdoerfer et al., 2001). Another study demonstrated a loss of NAPA homolog, NAPB, in brain specimens of adult patients with Down syndrome (Yoo et al., 2001).
  
  
Entity Huntington's disease
Note Marked elevation of NAPA expression was observed by Western blotting of hippocampus samples from patients with Huntington's diseases as compared to age-matched controls (Morton et al., 2001).
  
  
Entity Atopic dermatitis
Note A proteomic analysis of peripheral blood leukocytes demonstrated significant downregulation of NAPA expression in patients with atopic dermatitis as compared to control subjects (Kim et al., 2008). This decrease was validated by Western blotting analysis and NAPA level was suggested as a possible biomarker for the disease.
  

To be noted

Acknowledgments: the authors thank Alex Feygin for critical reading of the manuscript. This work was supported in part by National Institute of Health grants RO1 DK083968 and R01 DK084953 to A.I.I.

Bibliography

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Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1748-53. Epub 2004 Jan 30.
PMID 14755058
 
Vitamin E prevents hyperoxia-induced loss of soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor proteins in the rat neuronal cytoplasm.
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Biol Pharm Bull. 2013;36(9):1500-2.
PMID 23995663
 
Comparative proteomic analysis of peripheral blood mononuclear cells from atopic dermatitis patients and healthy donors.
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PMID 9647644
 
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Citation

This paper should be referenced as such :
Naydenov, NG ; Ivanov, AI
NAPA (N-ethylmaleimide-sensitive factor attachment protein, alpha)
Atlas Genet Cytogenet Oncol Haematol. 2014;18(5):301-305.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/NAPAID44025ch19q13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(1;17)(p36;q21) WNT3 or NSF/PRDM16
t(3;19)(q27;q13) NAPA/BCL6


External links

Nomenclature
HGNC (Hugo)NAPA   7641
Cards
AtlasNAPAID44025ch19q13
Entrez_Gene (NCBI)NAPA  8775  NSF attachment protein alpha
AliasesSNAPA
GeneCards (Weizmann)NAPA
Ensembl hg19 (Hinxton)ENSG00000105402 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000105402 [Gene_View]  chr19:47487634-47515258 [Contig_View]  NAPA [Vega]
ICGC DataPortalENSG00000105402
TCGA cBioPortalNAPA
AceView (NCBI)NAPA
Genatlas (Paris)NAPA
WikiGenes8775
SOURCE (Princeton)NAPA
Genetics Home Reference (NIH)NAPA
Genomic and cartography
GoldenPath hg38 (UCSC)NAPA  -     chr19:47487634-47515258 -  19q13.32-q13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)NAPA  -     19q13.32-q13.33   [Description]    (hg19-Feb_2009)
EnsemblNAPA - 19q13.32-q13.33 [CytoView hg19]  NAPA - 19q13.32-q13.33 [CytoView hg38]
Mapping of homologs : NCBINAPA [Mapview hg19]  NAPA [Mapview hg38]
OMIM603215   
Gene and transcription
Genbank (Entrez)AA542963 AA807920 AK098401 AK123456 AK126519
RefSeq transcript (Entrez)NM_003827
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)NAPA
Cluster EST : UnigeneHs.744881 [ NCBI ]
CGAP (NCI)Hs.744881
Alternative Splicing GalleryENSG00000105402
Gene ExpressionNAPA [ NCBI-GEO ]   NAPA [ EBI - ARRAY_EXPRESS ]   NAPA [ SEEK ]   NAPA [ MEM ]
Gene Expression Viewer (FireBrowse)NAPA [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8775
GTEX Portal (Tissue expression)NAPA
Protein : pattern, domain, 3D structure
UniProt/SwissProtP54920   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP54920  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP54920
Splice isoforms : SwissVarP54920
PhosPhoSitePlusP54920
Domains : Interpro (EBI)NSF_attach    TPR-like_helical_dom   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)NAPA
DMDM Disease mutations8775
Blocks (Seattle)NAPA
SuperfamilyP54920
Human Protein AtlasENSG00000105402
Peptide AtlasP54920
HPRD04447
IPIIPI00009253   
Protein Interaction databases
DIP (DOE-UCLA)P54920
IntAct (EBI)P54920
FunCoupENSG00000105402
BioGRIDNAPA
STRING (EMBL)NAPA
ZODIACNAPA
Ontologies - Pathways
QuickGOP54920
Ontology : AmiGOGolgi membrane  SNARE binding  soluble NSF attachment protein activity  protein binding  vacuolar membrane  cytosol  intracellular protein transport  ER to Golgi vesicle-mediated transport  retrograde vesicle-mediated transport, Golgi to ER  intra-Golgi vesicle-mediated transport  brain development  regulation of synaptic vesicle priming  membrane  syntaxin binding  neuron differentiation  SNARE complex  protein complex binding  synaptic transmission, glutamatergic  SNARE complex disassembly  terminal bouton  myelin sheath  apical protein localization  COPII vesicle coating  membrane fusion  synaptobrevin 2-SNAP-25-syntaxin-1a complex  extracellular exosome  
Ontology : EGO-EBIGolgi membrane  SNARE binding  soluble NSF attachment protein activity  protein binding  vacuolar membrane  cytosol  intracellular protein transport  ER to Golgi vesicle-mediated transport  retrograde vesicle-mediated transport, Golgi to ER  intra-Golgi vesicle-mediated transport  brain development  regulation of synaptic vesicle priming  membrane  syntaxin binding  neuron differentiation  SNARE complex  protein complex binding  synaptic transmission, glutamatergic  SNARE complex disassembly  terminal bouton  myelin sheath  apical protein localization  COPII vesicle coating  membrane fusion  synaptobrevin 2-SNAP-25-syntaxin-1a complex  extracellular exosome  
Pathways : KEGGSynaptic vesicle cycle   
REACTOMEP54920 [protein]
REACTOME PathwaysR-HSA-6811440 [pathway]   
NDEx NetworkNAPA
Atlas of Cancer Signalling NetworkNAPA
Wikipedia pathwaysNAPA
Orthology - Evolution
OrthoDB8775
GeneTree (enSembl)ENSG00000105402
Phylogenetic Trees/Animal Genes : TreeFamNAPA
HOVERGENP54920
HOGENOMP54920
Homologs : HomoloGeneNAPA
Homology/Alignments : Family Browser (UCSC)NAPA
Gene fusions - Rearrangements
Fusion : MitelmanNAPA/BCL6 [19q13.32/3q27.3]  
Fusion Cancer (Beijing)S100A8 [1q21.3]  -  NAPA [19q13.32]  [FUSC003481]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerNAPA [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)NAPA
dbVarNAPA
ClinVarNAPA
1000_GenomesNAPA 
Exome Variant ServerNAPA
ExAC (Exome Aggregation Consortium)NAPA (select the gene name)
Genetic variants : HAPMAP8775
Genomic Variants (DGV)NAPA [DGVbeta]
DECIPHERNAPA [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisNAPA 
Mutations
ICGC Data PortalNAPA 
TCGA Data PortalNAPA 
Broad Tumor PortalNAPA
OASIS PortalNAPA [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICNAPA  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDNAPA
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch NAPA
DgiDB (Drug Gene Interaction Database)NAPA
DoCM (Curated mutations)NAPA (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)NAPA (select a term)
intoGenNAPA
NCG5 (London)NAPA
Cancer3DNAPA(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603215   
Orphanet
MedgenNAPA
Genetic Testing Registry NAPA
NextProtP54920 [Medical]
TSGene8775
GENETestsNAPA
Target ValidationNAPA
Huge Navigator NAPA [HugePedia]
snp3D : Map Gene to Disease8775
BioCentury BCIQNAPA
ClinGenNAPA
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8775
Chemical/Pharm GKB GenePA31443
Clinical trialNAPA
Miscellaneous
canSAR (ICR)NAPA (select the gene name)
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineNAPA
EVEXNAPA
GoPubMedNAPA
iHOPNAPA
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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