Jump to content

User:Patel343/sandbox

From Wikipedia, the free encyclopedia

PRR16

Proline-rich protein 16 (PRR16) is a protein coding gene in Homo sapiens.[1] The protein is known by the alias Largen.

Gene

[edit]

Locus

[edit]

PRR16 is located on the long arm of chromosome 5. It is found at position 5q23.1. It has five known transcripts.[2]

Gene Neighborhood

[edit]

Cytogenic band: 5q23.1

[3]

The image above shows chromosome five and the various gene locations on it. PRR16 can be seen at the thin red band that has been placed at q23.

Size

[edit]

PRR16 spans 330,365 bases and encodes for a mRNA that is 1,707 nucleotides. The resulting protein is 304 amino acids long.[1]

mRNA

[edit]

Splice Variants

[edit]

PRR16 has five known splice variants, each with a different processed transcript. [4]

Isoforms

[edit]

There are three known isoforms of PRR16. Isoform 2 contains an additional exon in the 5' region, and it thus differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. Isoform 3 has two variants. The first contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The second contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. All three isoforms are shorter at the N-terminus, compared to isoform 1.[1]

Protein

[edit]

Structure

[edit]

Primary Structure

[edit]

The PRR16 protein is 304 amino acids in length. It has a molecular weight of 32.8 kDa and an isoelectric point of 8.09.[5][6] The protein does not interact with the membrane.

Secondary Structure

[edit]
α-helix from amino acid 38 to 52 of PRR16 determined by PHYRE2

The only predictable feature of the PRR16 protein is an α-helix near the N-terminus, spanning about thirty amino acids. The remainder of the protein is comprised of a disordered structure.[7]

Tertiary Structure

[edit]

This structure was predicted by analyzing the amino acid sequence using I-TASSER. The final result can be seen below.[8]

I-TASSER software was used to predict the tertiary structure of PRR16. The blue coils indicate the presence of α-helices, while the remainder is relatively disordered.

Post-Translational Modifications

[edit]
  • Predicted glycation at Lys 4, Lys 6, Lys 49, Lys 94, Lys 96, Lys 105, Lys 119, Lys 148, Lys 181, and Lys 290.[9]
  • Predicted nuclear export signals (NES) at Leu 39 and Leu 41.[10]
  • Predicted O-linked glycosylation sites at Ser 2, Ser 5, Ser 10, Ser 11, Ser 12, Ser 75, Thr 79, Ser 82, Ser 83, Ser 84, Ser 85, Thr, 87, Thr 88, Ser 91, Ser 111, Thr 130, Thr 143, Thr 149, Glu 235, Leu 254, Ser 270, Ser 272, Ser 274, Thr 282, Thr 287, Thr 294, Ser 299, and Thr 300.[11]
  • Predicted phosphorylation at Ser 2, Ser 5, Ser 10, Ser 11, Ser 22, Ser 74, Ser 75, Ser 82, Ser 83, Ser 84, Ser 85, Ser 97, Ser 91, Thr 115, Thr 130, Thr 152, Tyr 224, Thr 254, Thr 282, Ser 299, Thr 300, and Thr 303.[12]
  • Predicted sumoylation at site Lys 133.[13]

Subcellular Location

[edit]

The k-NN tool suggests the location of PRR16 in the nucleus of the cell with 52.2% certainty. The cytoplasm was predicted with 30.4% certainty, The following locations were predicted with 4.3% certainty: cytoskeleton, plasma membrane, mitochondria, and peroxisome.[14]

Expression

[edit]

The PRR16 gene is expressed at very low levels throughout the body. It is expressed in the skeletal muscle, heart, lung, skin, portions of the brain, and bone marrow.[15]

Interacting Proteins

[edit]
Protein Function[16] Tool
Abelson-interactor 2 (ABI2) Regulation of cell growth and actin filament reorganization Biogrid[17], IntAct[18], Mentha[19]
Amyloid precursor protein (APP) Caspase activation and degeneration of both neuronal cell bodies Biogrid, InnateDB[20], Mentha
Death-associated protein kinase 1 (DAPK1) Positive mediator of programmed cell death Biogrid, IntAct
Neural precursor cell expressed developmentally downregulated protein 4-like (NEDD4L) E3 ubiquitin-protein ligase Biogrid, InnateDB, Mentha
Neural precursor cell expressed developmentally downregulated protein 4 (NEDD4) E3 ubiquitin-protein ligase Biogrid, InnateDB
Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) Involved in gastrointestinal immunity Biogrid
Protein phosphatase 1 catalytic subunit alpha (PPP1CA) Cell division, regulation of glycogen metabolism, muscle contractility, and protein synthesis Biogrid, InnateDB, IntAct, Mentha
Protein phosphatase 1 catalytic subunit gamma (PPP1CC) Cell division, regulation of glycogen metabolism, muscle contractility, and protein synthesis Biogrid, InnateDB, Mentha
SMAD ubiquitin regulatory factor 1 (SMURF1) E3 ubiquitin-protein ligase Biogrid, Mentha

Homology

[edit]

Paralogs

[edit]
Unrooted phylogenetic tree of vertebrate and invertebrate PRR16 orthologs. All abbreviations are the first two letters of genus name and first letter of species name. Tree made with a Neighbor-Joining method using a ClustalW-formatted set of sequences as input.[21]

There are two isoforms of Inhibitory synaptic factor 1 that are known paralogs of PRR16.

Orthologs

[edit]

PRR16 is found in all classes of vertebrates, including mammals, birds, fish, reptiles and amphibians. The most distant ortholog of PRR16 is in Branchiostoma belcheri and Branchiostoma floridae, which diverged an estimated 684 million years ago.[22] The gene has not been found in any plants, fungi or single celled organisms. The table below compares the known orthologs.[23]

Organism Common Name Class Accession Number Sequence Identity Sequence Similarity
Homo sapiens Human Mammalia NP_001287712.1 100% 100%
Pan paniscus Bonobo Mammalia XP_003826752.1 99% 100%
Mus musculus House mouse Mammalia NP_001074693.1 93% 95%
Ochotona princeps American pika Mammalia XP_004586413.1 91% 94%
Vombatus ursinus Common wombat Mammalia XP_027730777.1 87% 81%
Podarcis muralis Common wall lizard Reptilia XP_028604016.1 88% 91%
Alligator sinensis Chinese alligator Reptilia XP_006033732.1 86% 89%
Chrysemys picta bellii Painted turtle Reptilia XP_005305197.1 88% 91%
Pogona vitticeps Central bearded dragon Reptilia XP_020659290.1 84% 86%
Pseudonaja textilis Eastern brown snake Reptilia XP_026576168.1 81% 84%
Gallus gallus Chicken Aves XP_001232593.3 81% 85%
Columba livia Rock pigeon Aves XP_005506281.1 85% 89%
Haliaeetus leucocephalus Bald eagle Aves XP_010560635.1 82% 86%
Empidonax traillii Willow flycatcher Aves XP_027735123.1 82% 86%
Nanorana parkeri High Himalaya frog Amphibia XP_018426570.1 71% 79%
Xenopus tropicalis Western clawed frog Amphibia XP_017946181.1 72% 79%
Lepisosteus oculatus Spotted gar fish Actinopterygii XP_006626913.1 65% 77%
Callorhinchus milii Australian ghostshark Chondrichthyes XP_007897515.1 64% 75%
Branchiostoma belcheri Lancelet Amphioxiformes XP_019614579.1 47% 78%
Branchiostoma floridae Lancelet Amphioxiformes XP_002601582.1 47% 78%

References

[edit]
  1. ^ a b c "PRR16 proline rich 16 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-06-17.
  2. ^ "Gene: PRR16 (ENSG00000184838) - Summary - Homo sapiens - Ensembl genome browser 97". useast.ensembl.org. Retrieved 2019-07-30.
  3. ^ "PRR16 Gene". www.genecards.org. Retrieved 2019-07-30.
  4. ^ "Ensembl genome browser 78: Homo sapiens - Summary - Gene: PRR16 (ENSG00000184838)". dec2014.archive.ensembl.org. Retrieved 2019-07-30.
  5. ^ "SAPS Results". www.ebi.ac.uk. Retrieved 2019-07-30.
  6. ^ "CALCULATION OF PROTEIN ISOELECTRIC POINT". isoelectric.org. Retrieved 2019-07-30.
  7. ^ "DisEMBL 1.5 - Predictors of intrinsic protein disorder". dis.embl.de. Retrieved 2019-08-01.
  8. ^ "I-TASSER results". zhanglab.ccmb.med.umich.edu. Retrieved 2019-08-01.
  9. ^ "NetGlycate 1.0 Server - prediction results". www.cbs.dtu.dk. Retrieved 2019-08-04.
  10. ^ "NetNES 1.1 Server - prediction results". www.cbs.dtu.dk. Retrieved 2019-08-04.
  11. ^ "NetOGlyc 4.0 Server - prediction results". www.cbs.dtu.dk. Retrieved 2019-08-04.
  12. ^ "NetPhos 3.1 Server - prediction results". www.cbs.dtu.dk. Retrieved 2019-08-04.
  13. ^ "GPS-SUMO: Prediction of SUMOylation Sites & SUMO-interaction Motifs". sumosp.biocuckoo.org. Retrieved 2019-08-04.
  14. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2019-08-01.
  15. ^ "GDS3113 / 202795". www.ncbi.nlm.nih.gov. Retrieved 2019-08-01.
  16. ^ "STRING: functional protein association networks". string-db.org. Retrieved 2019-08-04.
  17. ^ "PRR16 Result Summary | BioGRID". thebiogrid.org. Retrieved 2019-08-04.
  18. ^ "PRR16 Interactions".
  19. ^ "Results - mentha: the interactome browser". mentha.uniroma2.it. Retrieved 2019-08-04.
  20. ^ al, David Lynn et. "InnateDB: Systems Biology of the Innate Immune Response". www.innatedb.com. Retrieved 2019-08-04.
  21. ^ "Multiple Sequence Alignment - CLUSTALW". www.genome.jp. Retrieved 2019-07-03.
  22. ^ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2019-07-01.
  23. ^ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2019-08-01.
Retrieved from "https://en.wikipedia.org/w/index.php?title=User:Patel343/sandbox&oldid=1091953030"