Ubiquitin carboxyl-terminal hydrolase MINDY-2 is an enzyme which in humans is encoded by the gene MINDY2 (previously FAM63B). MINDY-2 functions to remove ubiquitin from proteins (specifically 'Lys-48'-linked conjugated ubiquitin), and may be involved in regulating the turnover of proteins in cells.
Gene
Locus FAM63B is located at 15q21.3-q22.1, spanning 90,707 base pairs on chromosome 15.
Alternative Names The full name of FAM63B is family with sequence similarity 63, member B. FAM63B is also listed by its alias, KIAA1164, in some publications.
mRNA
Isoforms The FAM63B gene encodes a primary transcript that can be alternatively spliced into 9 protein variants. FAM63B variant a is the most common isoform found in humans. Variant Length (amino acids) Exon Count Molecular Weight (kdal) Isoelectric Point a 621 9 67.1 4.24 b 620 9 67.0 4.24 x1 639 10 69.2 4.40 x2 638 10 69.1 4.40 x3 605 10 65.2 4.41 x4 587 9 63.1 4.25 x5 364 6 38.0 4.50 x6 351 8 40.2 4.72 x7 342 8 39.1 4.45http://seqtool.sdsc.edu/CGI/BW.cgi#!
Protein
Structure
Primary Structure FAM63B is a member of the Pfam super family, and contains a domain of unknown function (DUF544) that is homologous within the protein family. FAM63B protein variant an also contains a bipartite tryptophan binding motif from W476 to W533.Dodding, M. P., Mitter, R., Humphries, A. C., & Way, M. (2011). A kinesin-1 binding motif in vaccinia virus that is widespread throughout the human genome. The EMBO Journal, 30(22), 4523–4538. http://doi.org/10.1038/emboj.2011.326 Variant a of the protein also contains a hydrophobic stretch of alanine from 567 to 574 and a mixed charge sequence from residue 598 to 617. FAM63B protein may contain a signal sequence specifying return to the endoplasmic reticulum (KDEL) from residue 607 to 621 in variant a.
Secondary Structure The secondary structure of FAM63B is a combination of coils, some α-helices, and few β-sheets. The Phyre 2 program predicts α-helices in 23% of the protein, β-strands in 9% of the protein, and the remaining 59% of the protein as disordered. The disordered regions coincide with the coiled regions predicted by other programs, and this results in the long stretch of coiled protein beginning at the N-terminus. According to the SOUSI program, there is a 16-amino acid-long span from residues 265 to 280 of FAM63B that could be a transmembrane sequence. However, transmembrane sequences generally need to be at least 20 amino acids long in order to be stable in the membrane, so a transmembrane sequence is unlikely. Therefore, FAM63B is not fixed in the membrane of any organelle and is free to move through the cell and between organelles.
Tertiary Structure Not much is known about the tertiary structure of FAM63B. A predicted folding is shown.
Post-translational Modifications Post-translational modifications of the FAM63B protein. Post-translational Modification Site(s) Impact on Protein Acetylation Ser3 Stability, localization, metabolism, apoptosis, ribosome recognition for synthesis Lysine Glycation Lys88, Lys251, Lys280, Lys282, Lys332, Lys393, Lys398, Lys454, Lys547 Impaired function, changed characteristics Phosphorylation Ser7, Ser21, Ser25, Ser26, Ser62, Ser66, Ser68, Ser72, Ser90, Ser94, Ser111, Ser148, Ser153, Ser158, Ser160, Ser165, Ser170, Ser175, Ser188, Ser193, Ser233, Ser396, Ser440, Ser499, Ser541, Ser558, Ser587, Ser589, Ser590, Ser594, Ser597, Thr48, Thr255, Thr344, Thr453, Tyr505 Conformation change, turn enzymatic activity on/off Picornaviral Cleavage Glu195, Gln535 Cleavage of polyprotein, degradation O-GlcNAc Ser3, Ser21, Ser49, Ser62, Ser66, Ser68, Ser80, Ser152, Ser153, Ser158, Ser170, Ser499, Ser575, Ser587, Ser589, Ser590, Thr144, Thr576 Nucleocytoplasmic location
Subcellular Location FAM63B has predicted NES (nuclear export signals) at Val274 and Leu277. Also, a NLS (nuclear localization signal) is predicted for FAM63B at RKRK at residue 599. In agreement, Reinhardt's method for cytoplasmic/nuclear discrimination predicts FAM63B to be located in the nucleus with a reliability of 76.7%. The presence of both NLS and NES signals and O-GlcNAc post-translational modification of FAM63B supports the protein's location in both the nucleus and cytoplasm and the discovered protein function as a shuttle for vaccinia virus between the nucleus and the cell periphery.
Expression
Expression Level FAM63B has moderately-high to high expression and is constitutively expressed. FAM63B is likely ubiquitously expressed in humans.
Differential Expression Expression of FAM63B is high in the embryonic stem cells and differentiated tissues but low or off in embryoid bodies and other progenitor cells, such as the multipotent mesenchymal stem cells. It is likely that FAM63B is expressed during pluripotency and unipotency but is not important for differentiation, as is occurring in embryoid bodies, mesenchymal stem cells, and other progenitor cells.
Regulation of Expression
Transcriptional Regulation The promoter of FAM63B is GXP_5885, located on the positive strand of chromosome 15 from (58770692, 58771462) and is 711 base pairs long.
Interacting Proteins FAM63B is shown to interact with one protein, KLC-1.Dodding, M. P., Mitter, R., Humphries, A. C., & Way, M. (2011). A kinesin-1 binding motif in vaccinia virus that is widespread throughout the human genome. The EMBO Journal, 30(22), 4523–4538. http://doi.org/10.1038/emboj.2011.326 KLC-1, kinesin light chain 1, is a protein which recruits kinesin-1 via its cargo binding light chain and contains a bipartite tryptophan binding motif. This motif is present in a vaccinia virus integral membrane protein, A36, that is required for transport of the virus from the perinuclear space to the cell periphery. In the absence of A36, proteins with a bipartite tryptophan binding motif can interact with the kinesin light chain, recruit KLC-1, and promote virus transport from the nucleus to the cytoplasm.
Function The discovered function of FAM63B protein is a transporter of vaccinia virus in the human genome. FAM63B contains a bipartite tryptophan binding motif between W476 and W533. The motif also contains a Q residue at the +2 position, which was found to be a frequent occurrence in proteins that bind KLC-1 or KLC-2. FAM63B is among proteins studied that can rescue virus transport to the cell periphery when expressed in A36-deficient cells, successfully replacing the cytoplasmic domain A36 of vaccinia.
Clinical Significance
Pathology The specific pathology of FAM63B is unknown.
Disease Association FAM63B is part of four networks regulated by miRNA, three of which are linked to neuronal differentiation and dopaminergic gene expression.Aberg, K. A., et al. (2014). Methylome-Wide Association Study of Schizophrenia. JAMA Psychiatry, 71(3), 255–264. http://doi.org/10.1001/jamapsychiatry.2013.3730 These findings indicate that FAM63B could be used as a biomarker for the detection and treatment of schizophrenia. Furthermore, aberrant methylation of FAM63B may play a role in the development of schizophrenia. FAM63B has also been ranked 13 of 25 on a list of associated genes relevant to arthritis.Li, C., et al. (2008). A systematic method for mapping multiple loci: An application to construct a genetic network for rheumatoid arthritis. Gene, 408(1–2), 104–111. http://doi.org/10.1016/j.gene.2007.10.028
Homology
Paralogs FAM63B has one paralog, FAM63A, which is a gene of unknown function. FAM63A gene encodes a protein that is 469 amino acids long and 76% similar to FAM63B.
Orthologs FAM63B has been found in all multicellular and unicellular eukaryotes, including plants but excluding protists and fungi. The gene has also been found in archaea but not bacteria. Genus & species Common name Date of Divergence from Humans (MYA) Accession number Sequence length (amino acids) ! !Sequence similarity to Human Protein (%) Clade Pan troglodytes Chimpanzee 6.2 XP_510443.2 621 100 Mammalia Microtus ochrogaster Prairie vole 90.1 XP_005347720.1 597 84 Mammalia Ursus maritimus Polar bear 95 XP_008704293.1 591 97 Mammalia Acinonyx jubatus Cheetah 95 XP_014926357.1 488 96 Mammalia Pelodiscus sinensis Green sea turtle 320.5 XP_014434471.1 408 95 Reptilia Zonotrichia albicollis White-throated sparrow 320.5 XP_014123064.1 326 91 Aves Columba livia Rock dove 320.5 XP_005511195.1 340 91 Aves Chrysemys picta bellii Western painted turtle 320.5 XP_008162326.1 566 86 Reptilia Melopsittacus undulatus Budgerigar 320.5 XP_005145999.1 472 86 Aves Xenopus tropicalis Western clawed frog 354.4 XP_002937714.1 354 87 Amphibia Latimeria chalumnae Western Indian Ocean coelacanth 413.69 XP_005998789.1 652 83 Sarcopterygii Lepisosteus oculatus Spotted gar 436.8 XP_015198676.1 642 82 Actinopterygii Hydra vulgaris Hydra 902 XP_012556960.1 507 65 Hydrozoa Octopus bimaculoides California two-spot octopus 903 XP_014779548.1 981 58 Cephalopoda Crassostrea gigas Pacific oyster 903 XP_011440367.1 569 71 Bivalvia Haemonchus contortus Barber's pole worm 903 CDJ97151.1 437 55 Secernentea Trichoplax adhaerens Trichoplax 936 XP_002108532.1 308 75 Placozoa Solanum pennellii Tomato 1570.5 XP_015085752.1 686 65 Angiosperms Sesamum indicum Sesame 1570.5 XP_011071984.1 738 65 Angiosperms Thermoplasmatales archaeon BRNA1 4250 WP_048164282.1 1063 39 Archaea
Distant Homologs The most distant homolog of FAM63B is found in Thermoplasmatales archaeon, an archaea that diverged from the human gene 4.25 billion years ago.
Homologous Domains FAM63B is a member of the Pfam super family, and contains a domain of unknown function (DUF544) homologous within the protein family. This region of the protein is highly conserved through FAM63B homologs, as is the bipartite tryptophan binding motif of FAM63B and the C-terminus signal sequence.
Phylogeny The phylogenetic tree below shows a time calibration for the evolution of FAM63B.
References