NKAPD1

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NKAPD1
Identifiers
AliasesNKAPD1, C11orf57, chromosome 11 open reading frame 57, NKAP domain containing 1
External IDsMGI: 2143205 HomoloGene: 41233 GeneCards: NKAPD1
Orthologs
SpeciesHumanMouse
Entrez

55216

270156

Ensembl

ENSG00000150776

ENSMUSG00000059820

UniProt

Q6ZUT1

n/a

RefSeq (mRNA)

NM_001134902
NM_212449
NM_001360340

RefSeq (protein)

n/a

Location (UCSC)Chr 11: 112.07 – 112.09 MbChr 9: 50.52 – 50.53 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

NKAPD1 (NF-kappa-B-activating protein domain containing 1) is a protein, which in humans, is encoded by the gene NKAPD1. This protein is also commonly referred to as C11ORF57 (Chromosome 11 Open Reading Frame 57).[5]

Gene[edit]

The NKAPD1 gene is found on human chromosome 11 at locus 11q23.1 with plus strand orientation. The exact location is 112,074,086 to 112,085,150, spanning a total of 11,065 base pairs, including introns.[5][6]

It can be transcribed into 7 different transcript variants resulting in 4 different isoforms of the protein. The longest mRNA transcript contains a total of 6 exons. [6]

Gene neighborhood[edit]

The human NKAPD1 gene is closely surrounded by the following genes on chromosome 11.[7]

  • DLAT
  • PIH1D2
  • TIMM8B
  • SDHD

Gene expression[edit]

The human NKAPD1 gene is ubiquitously expressed at moderate levels in various normal tissues throughout the body, with higher expression in the brain and thyroid.[6][8]

Protein[edit]

Transcripts[edit]

The longest protein isoform produced by the human NKAPD1 gene is known as isoform a and it is 293 amino acids long. This particular protein isoform has a predicted molecular weight around 34 kDa.[5] [6]

Transcript Variants and Protein Isoforms of NKAPD1[6]
Transcript Variant Isoform mRNA Accession # mRNA Length Protein Accession # Protein Length Notes
1 isoform a NM_018195.4 3686 nt NP_060665.3 293 aa Longest isoform and mRNA
2 isoform a NM_001082969.2 3128 nt NP_001076438.1 293 aa Different in 5’ UTR
3 isoform b NM_001082970.2 3683 nt NP_001076439.1 292 aa Alternate splice site in 3’ coding region
4 N/A NR_103469.2 3727 nt N/A N/A Non-coding RNA
5 isoform b NM_001301017.2 3125 nt NP_001287946.1 292 aa Alternate splice site at 5’ end of last exon
6 isoform c NM_001301019.2 3169 nt NP_001287948.1 264 aa Alternate exons 1 and 2, uses alternate start codon
7 isoform d NM_001301021.2 3166 nt NP_001287950.1 263 aa Alternate exons 1 and 2

Domains[edit]

The human NKAPD1 protein contains one domain called the NKAP (NF-kappa-B-activating protein) domain. It also has a lysine rich region directly following the NKAP domain.[9][10]

Predicted three-dimensional structure of human NKAPD1 protein from AlphaFold, annotated with iCn3D.[11][12]

Structure[edit]

Secondary structure predictions suggest that the NKAPD1 protein consists mainly of alpha helices.[13] Predicted three-dimensional structures showed mostly coils with a few small regions of alpha helices. [11]

Post-translational modifications[edit]

The human NKAPD1 protein is predicted to undergo SUMOylation at several different lysines as well as phosphorylation, acetylation, and N-myristoylation at different amino acids. [10]

Homology and evolution[edit]

Orthologs[edit]

Orthologs to the human NKAPD1 gene can be found in all vertebrates through sharks, rays, and lampreys, however it is not found in any invertebrates. This gene is shown to be very highly conserved in mammals.[6][14]

Table of strict and distant orthologs to the human NKAPD1 protein. Organized by median date of divergence and percent sequence identity to the human protein.
Table of strict and distant orthologs to the human NKAPD1 protein. Organized by median date of divergence and percent sequence identity to the human protein.
Graph showing the mutation rate per 100 residues of NKAPD1 gene in comparison to fibrinogen alpha and cytochrome c. [6][15][16]

Evolution[edit]

When compared to fibrinogen alpha and cytochrome c, the human NKAPD1 gene seems to be evolving at a fairly moderate rate. [6][15][16]

Interacting proteins[edit]

There were 8 proteins found to have potential interactions with the human NKAPD1 protein. The table below shows the possible relationships between these proteins and the human NKAPD1 protein.[17]

Table of NKAPD1 Interacting Proteins (Organized by Score)[17]
Name Full Name Basis Score Function Tissue Expression Subcellular Localization
CSNK2A1 casein kinase 2 alpha 1 Experimental/Biochemical Data 0.615 Regulates numerous cellular processes Ubiquitous nucleus
PNN pinin Co-Expression, Experimental/Biochemical Data 0.570 Component of multiprotein exon junction complex Ubiquitous nucleus
DHX8 DEAH-box helicase 8 Experimental/Biochemical Data 0.563 facilitates nuclear export of spliced mRNA Ubiquitous nucleus
C9orf78 Chromosome 9 open reading frame 78 Co-Expression, Experimental/Biochemical Data 0.541 regulation of telomere assembly and telomere length Ubiquitous nucleus
RP9 RP9 pre-mRNA splicing factor Co-Expression, Experimental/Biochemical Data 0.527 Target protein for PM1 kinase, B-cell proliferation Ubiquitous nucleus, vesicles, and cytosol
CSNK2A2 casein kinase 2 alpha 2 Co-Expression, Experimental/Biochemical Data 0.505 Regulates numerous cellular processes testes nucleus
SREK1IP1 SREK1 interacting protein 1 Co-Expression, Experimental/Biochemical Data 0.502 Possible splicing regulator related to cell survival Ubiquitous nucleus
SYF2 SYF2 pre-mRNA splicing factor Co-Expression, Experimental/Biochemical Data 0.482 component of spliceosome, pre-mRNA splicing Ubiquitous nucleus

Clinical significance[edit]

Preliminary findings in three published studies suggest that deletion of the NKAPD1 gene, both complete and partial, are associated with the development of paraganglioma, a rare tumor of the head and neck. This research suggest that these deletions often occur hand-in-hand with deletions of several other nearby genes as well, most prominently SDHD, DLAT, PIHD2, and TIMM8B.[18][19][20]

References[edit]

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000150776 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000059820 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c "GeneCards". Retrieved December 17, 2023.
  6. ^ a b c d e f g h "NKAPD1 NKAP domain containing 1 [ Homo sapiens (human) ]". NCBI Gene. Retrieved December 17, 2023.
  7. ^ "UCSC Genome Browser". Retrieved December 15, 2023.
  8. ^ "c11orf57 GEO Profiles". NCBI GEO. Retrieved December 15, 2023.
  9. ^ "uncharacterized protein NKAPD1 isoform a [Homo sapiens]". NCBI Protein. Retrieved December 15, 2023.
  10. ^ a b "Motif Scan". MyHits Motif Scan. Retrieved December 10, 2023.
  11. ^ a b "AlphaFold Protein Structure Database". Retrieved December 4, 2023.
  12. ^ "iCn3D". NCBI. Retrieved December 4, 2023.
  13. ^ "I-TASSER". Zhang Lab. Retrieved December 4, 2023.
  14. ^ "EMBOSS Needle". EMBL-EBI. Retrieved December 17, 2023.
  15. ^ a b "FGA fibrinogen alpha chain [ Homo sapiens (human) ]". NCBI Gene. Retrieved December 17, 2023.
  16. ^ a b "CYCS cytochrome c, somatic [ Homo sapiens (human) ]". NCBI Gene. Retrieved December 17, 2023.
  17. ^ a b "STRING-DB". STRING. Retrieved December 17, 2023.
  18. ^ Cadiñanos J, Llorente JL, de la Rosa J, Villameytide JA, Illán R, Durán NS, et al. (August 2011). "Novel germline SDHD deletion associated with an unusual sympathetic head and neck paraganglioma". Head & Neck. 33 (8): 1233–1240. doi:10.1002/hed.21384. PMID 20310044. S2CID 24385357.
  19. ^ Bayley JP, Weiss MM, Grimbergen A, van Brussel BT, Hes FJ, Jansen JC, et al. (September 2009). "Molecular characterization of novel germline deletions affecting SDHD and SDHC in pheochromocytoma and paraganglioma patients". Endocrine-Related Cancer. 16 (3): 929–937. doi:10.1677/ERC-09-0084. PMID 19546167.
  20. ^ Hoekstra AS, van den Ende B, Julià XP, van Breemen L, Scheurwater K, Tops CM, et al. (April 2017). "Simple and rapid characterization of novel large germline deletions in SDHB, SDHC and SDHD-related paraganglioma". Clinical Genetics. 91 (4): 536–544. doi:10.1111/cge.12843. hdl:1887/116006. PMID 27485256.
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