Kinase Group SAPPK

Kinase Classification: Group SAPPK

SAPPK, or Structurally Atypical Putative Protein Kinases is a set of putative kinases that have been reported to have biochemical kinase activity, but have no structural relationship to any known kinase domain and no known mechanism of phosphotransfer. SAPPK contains the remainder of the old Atypical group of kinases, after the removal of members of the PKL, HisK and NDK groups. Some previous members of this group (H11, A6) have been later shown to lack kinase activity, and for several more members it remains possible that the demonstrated kinase activity was due to a contaminating typical kinase. Several are only known to autophosphorylate, and may have limited substrate range or in vivo function.

TAF: TATA binding factor associated factors

TAF1 (TAF II-250) is a component of the basal transcriptional machinery, and exists as a single copy gene in all fully-sequenced eukaryotes. It has no close homologs. TAF1 was reported to be a protein kinase with two regions which can independently phosphorylate the basal transcription factor RAP74 [1]. In vitro kinase assays were carried out with immunopurified TFIID from Hela cells or with cloned TAF1 transfected into insect Sf9 cells or E. coli. Deletion mapping showed that two independent regions, each less than 470 AA long had kinase activity, though neither had significant sequence similarity to each other, to protein kinases, or to any other proteins. Later studies [2, 3] confirm the result and perform a finer mapping of the N-terminal kinase region. TAF1L, is a retrotransposed copy of TAF1 present in human and old-world primates, which is expressed during spermatogenesis and substitutes for TAF1 in a cellular assay [4].

BCR

Best known as the fusion partner of the Abl kinase in chronic myologenous leukemia, BCR itself has repeatedly shown kinase activity in immunoprecipitated samples.

BRD: Bromodomain Kinases

This family of dual-bromodomain proteins have been reported as RNA polymerase C-terminal domain kinases.

FASTK

The human Fas-Activated S/T Kinase (FASTK, aka FAST) was characterised as a kinase which was dephosphorylated and activated during Fas-mediated apoptosis [5]. The nuclear TIA-1 RNA-binding protein, a putative apoptosis effector, was identified as a binding partner and substrate, using FASTK immunoprecipitated from COS cells. To control from contaminating binding proteins, the immunoprecipitate was run on SDS-PAGE, blotted and renatured, and shown to still have autophosphorylating kinase activity. A closely-comigrating band (60 kDa vs. 65 kDa for FASTK) was seen in the initial kinase assay, but not in the renatured assay, suggesting that it might be a contaminating kinase that could migrate on the blot to phosphorylate FASTK (as seen elsewhere for H11). This paper also shows an alignment of FASTK to H11 and PKA to attempt to define catalytic motifs, but the alignment is unconvincing and the predicted catalytic residues are generally not conserved in FASTK orthologs and paralogs (the overall sequence conservation is low, with only one G and one D absolutely conserved in the family within vertebrates, unlikely for an enzyme requiring multiple active site residues) .

Similar IP'd kinase activities were seen in a follow up [6], but the kinase activity has not been further scrutinized. A screen for SH3 domain-interacting proteins [7] found FASTK to interact with the CRK SH3 domain, which could couple FASTK to tyrosine kinases. This is supported by two proteomic screens that found Y532 to be phosphorylated, and the NetPhorest analysis indicates that this is likely to be an Abl-related kinase substrate site. The kinase activity associated with FASTK was S/T specific, so Abl is unlikely to be the protein associated with this activity.

G11 (STK19)

This family consists of a single human gene shown once to have serine/threonine kinase activity against alpha casein and histone when immunoprecipitated from insect or mammalian cells.

TIF1: Transcriptional Intermediary Factor 1

This is a family of four mammalian genes (TIF1a,b,g, d, aka TRIM24, TRIM28, TRIM33, TRIM66), of which TIF1a and TIF1b have been shown to have protein kinase activity [8, 9]. A single TIF1 exists in Drosophila and Nematostella but not in C. elegans.

His-tagged TIF1 was expressed by bacculovirus in Sf9 cells, purified by DEAE-Sephadex, followed by a nickel affinity purification, and immunoprecipitated by 3 different TIF1a antibodies. Silver-staining of an SDS-PAGE gel showed only a single protein, and an in-gel kinase activity produced only one band, at the TIF1a size. The purified TIF1a was shown to autophosphorylate and to phosphorylate several basal transcription factors and heterochromatin proteins (HPs). TIF1a purified with a single antibody gave a similar result.

Like the TAFs, TIFs are involved in the transcriptional machinery. Also similar to the TAFs and to BRD kinases, the TIFs contain bromodomains, suggesting that they may be in some way inovlved in the kinase functions of these proteins.

The TIFs have no sequence similarity to known kinases except in their bromodomains, and have not been dissected to see where the kinase activity lies. However, the high stringency of purification makes them better candidates to be genuine kinases than several of the other atypical kinases reported.

BAZ

The WSTF/BAZ1B gene ("Bromodomain adjacent to zinc finger domain, 1B") was shown in 2009 [10] to phosphorylate Histone H2A.X on Tyr142. This residue is dephosphorylated by the eyes absent phosphatases, and is involved in DNA damage repair. The activity was found in recombinant BAZ1B protein purified from insect cells and found to be almost fully pure by mass spectrometry. Deletion analysis mapped the kinase activity to the first 345 residues of the protein, which contains a WAC domain and a C-terminal domain of conserved sequence. Expression of both domains separately (N-term: 1-205; C-term: 208-345) in E. coli indicated that the kinase activity residues in the WAC domain but is enhanced by the presence of the C-terminal domain.

BAZ1B is a deuterostome-specific protein and a homolog of BAZ1A which is found in almost all eukaryotes. Cys338 was shown to be required for full kinase activity, but is found only in mammalian and avian copies of BAZ1B. The protein also includes a bromodomain, which is also found in several other atypical kinases: BRD, TAF1 and TIF1.

COL4A3BP

Protein involved in ER/Golgi ceramide transport. The human form has also been shown in two papers to have autophosphoryation activity.

BLVRA: Biliverdin Reductase A

Best known as the enzyme that reduces biliverdin to bilrubin, as part of bile acid production and a possible celular redox cycle. Iit has also been implicated in Insulin receptor signaling, MAPK activity, PKC activation and even as a transcription factor and is reported to autophosphorylate in vitro.

RAD51B

RAD51B is a homolog of the DNA repair protein RAD51 which was shown in one report to have protein kinase activity. It contains a P-loop NTPase fold.

GAPDH

The glycolytic enzyme, Glyceraldehyde-3-phosphate dehydrogenase has been demonstrated to have a kinase activity towards viral proteins, a GABA receptor, and in vitro.

TGM

Tissue Transglutaminase 2 (TGM2) is a multi-functional protein that has been reported in human to phosphorylate several proteins, including p53, Histones and Rb.

Likely non-kinases

Several proteins have been demonstrated to show biochemical activity, despite the lack of sequence similarity to any other kinases. The original kinome catalogs [11, 12] included any proteins with at least one credible report of kinase activity. Since then, a lack of any follow-on studies, and weaknesses in the original studies suggest that these proteins are unlikely to be kinases. Their observed activity in many cases may have been due to a contaminating kinase protein. In the case of Twinfilin/A6 and H11 there is now published evidence arguing against their kinase activity, and the case of H11 in particular shows how even stringent biochemical methods to avoid contamination can fail. The others in this list have weak evidence for their kinase activity, and/or little or no follow-up to the original studies.

Twinfilin/A6

Twinfilin is a actin monomer-binding protein. It was once reported to be a tyrosine kinase, but two independent groups have failed to replicate this finding, and so this family has been removed from the kinome (more...)

H11

Human H11 gene and a viral homolog, ICP10, have both been associated with kinase activity, using very credible assays. However, careful follow-up studies now cast doubt on all these data, making for a cautionary tale for the interpretation of biochemical results (more...)

CPNE3: Copine 3

Copines are found in most eukaryotes, with nine members in human. They have twin C2 domains and a VWA domain that has a Rossman fold (a possible nucleotide binding fold). Copines interact with phospholipids in a calcium-dependent manner. A single paper [13] demonstrated kinase activity in human Copine 3. Protein was immunoprecipitated or affinity purified from human cells and found to phosphorylate MBP in both solution and in-gel assays. Tagged protein, affinity purified from yeast also had activity, but E. coli-expressed protein did not. The same antibody (a polyclonal against an 18-AA C-terminal peptide) was used both for pulldown and affinity purification, and showed one contaminating band, at 70kDa. The specific activity was low (estimated as fmol/min/mg). This low rate, the presence of a contaminating band in the immunopreciptates and lack of kinase activity when purified from E. coli are suggestive of the kinase activity being due to a co-purified kinase. However, it is possible that the low activity and lack of E. coli activity are due to a lack of proper folding (the coli extract was largely insoluble), a required posttranslational modification or a (non-kinase) activating subunit. CPNE3 also specifically binds Y1248-phosphorylated ErbB2 [14], through phospho-Y1248 and to be required for ErbB2 activation of Src in some circumstances. It also colocalizes with FAK and is upregulated in ErbB2-amplified tumors. The related CPNE1 was shown in high-throughput interaction screens to bind MEK1 (MAP2K1) and phosphatase PPP5C [15], suggesting MEK1 as a potential contaminating kinase.

GTF2F1/TFIIFa

This general transcription factor was shown to autophosphorylate in vitro [16], using chromatographically- and immuno-purified protein from HeLa extracts, or from a bacculovirus/Sf9 expression system. In both cases, the TFIIFb subunit was co-purified, but no other bands were seen (by Coomassie stain). In-gel kinase assays showed the expected phosphorylation band, after separation from TFIIFb. Phosphorylation was mapped to two sites, S385 and T389. No transposphorylation was seen either of promiscuous substrates (Histone H1, Casein) or several transcription-associated proteins. TFIIFa is also phosphorylated by TAF1 and CK2, though on distinct sites, so co-purification of these kinases would not account for the observed autophosphorylation. Expression of TFIIFa alone in Sf9 cells gave higher activity, suggesting that TFIIFb is a repressor of kinase activity. Activity was also inhibited by the adenosine analog DRB ( 5,6-dichloro-1-b-D-ribofurano-sylbenzimidazole). Caveats with this validation include the lack of stringent controls on co-purifying kinases (e.g. silver stain, or bacterial expression), and the possibility that the in-gel assay was compromised by migration of a separate kinase to the substrate site (as seen in H11).

References

1. Dikstein R, Ruppert S, and Tjian R. TAFII250 is a bipartite protein kinase that phosphorylates the base transcription factor RAP74. Cell. 1996 Mar 8;84(5):781-90. DOI:10.1016/s0092-8674(00)81055-7 |
2. Solow S, Salunek M, Ryan R, and Lieberman PM. Taf(II) 250 phosphorylates human transcription factor IIA on serine residues important for TBP binding and transcription activity. J Biol Chem. 2001 May 11;276(19):15886-92. DOI:10.1074/jbc.M009385200 |
3. O'Brien T and Tjian R. Functional analysis of the human TAFII250 N-terminal kinase domain. Mol Cell. 1998 May;1(6):905-11. DOI:10.1016/s1097-2765(00)80089-1 |
4. Wang PJ and Page DC. Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. Hum Mol Genet. 2002 Sep 15;11(19):2341-6. DOI:10.1093/hmg/11.19.2341 |
5. Tian Q, Taupin J, Elledge S, Robertson M, and Anderson P. Fas-activated serine/threonine kinase (FAST) phosphorylates TIA-1 during Fas-mediated apoptosis. J Exp Med. 1995 Sep 1;182(3):865-74. DOI:10.1084/jem.182.3.865 |
7. Wu C, Ma MH, Brown KR, Geisler M, Li L, Tzeng E, Jia CY, Jurisica I, and Li SS. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Proteomics. 2007 Jun;7(11):1775-85. DOI:10.1002/pmic.200601006 |
8. Fraser RA, Heard DJ, Adam S, Lavigne AC, Le Douarin B, Tora L, Losson R, Rochette-Egly C, and Chambon P. The putative cofactor TIF1alpha is a protein kinase that is hyperphosphorylated upon interaction with liganded nuclear receptors. J Biol Chem. 1998 Jun 26;273(26):16199-204. DOI:10.1074/jbc.273.26.16199 |
9. Nielsen AL, Ortiz JA, You J, Oulad-Abdelghani M, Khechumian R, Gansmuller A, Chambon P, and Losson R. Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family. EMBO J. 1999 Nov 15;18(22):6385-95. DOI:10.1093/emboj/18.22.6385 |
10. Xiao A, Li H, Shechter D, Ahn SH, Fabrizio LA, Erdjument-Bromage H, Ishibe-Murakami S, Wang B, Tempst P, Hofmann K, Patel DJ, Elledge SJ, and Allis CD. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature. 2009 Jan 1;457(7225):57-62. DOI:10.1038/nature07668 |
11. Manning G, Plowman GD, Hunter T, and Sudarsanam S. Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci. 2002 Oct;27(10):514-20. DOI:10.1016/s0968-0004(02)02179-5 |
12. Manning G, Whyte DB, Martinez R, Hunter T, and Sudarsanam S. The protein kinase complement of the human genome. Science. 2002 Dec 6;298(5600):1912-34. DOI:10.1126/science.1075762 |
13. Caudell EG, Caudell JJ, Tang CH, Yu TK, Frederick MJ, and Grimm EA. Characterization of human copine III as a phosphoprotein with associated kinase activity. Biochemistry. 2000 Oct 24;39(42):13034-43. DOI:10.1021/bi001250v |
14. Heinrich C, Keller C, Boulay A, Vecchi M, Bianchi M, Sack R, Lienhard S, Duss S, Hofsteenge J, and Hynes NE. Copine-III interacts with ErbB2 and promotes tumor cell migration. Oncogene. 2010 Mar 18;29(11):1598-610. DOI:10.1038/onc.2009.456 |
15. Tomsig JL, Snyder SL, and Creutz CE. Identification of targets for calcium signaling through the copine family of proteins. Characterization of a coiled-coil copine-binding motif. J Biol Chem. 2003 Mar 21;278(12):10048-54. DOI:10.1074/jbc.M212632200 |
16. Rossignol M, Keriel A, Staub A, and Egly JM. Kinase activity and phosphorylation of the largest subunit of TFIIF transcription factor. J Biol Chem. 1999 Aug 6;274(32):22387-92. DOI:10.1074/jbc.274.32.22387 |
17. Brutsche MH, Brutsche IC, Wood P, Brass A, Morrison N, Rattay M, Mogulkoc N, Simler N, Craven M, Custovic A, Egan JJ, and Woodcock A. Apoptosis signals in atopy and asthma measured with cDNA arrays. Clin Exp Immunol. 2001 Feb;123(2):181-7. DOI:10.1046/j.1365-2249.2001.01441.x |
18. Machius M, Chuang JL, Wynn RM, Tomchick DR, and Chuang DT. Structure of rat BCKD kinase: nucleotide-induced domain communication in a mitochondrial protein kinase. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11218-23. DOI:10.1073/pnas.201220098 |
19. Steussy CN, Popov KM, Bowker-Kinley MM, Sloan RB Jr, Harris RA, and Hamilton JA. Structure of pyruvate dehydrogenase kinase. Novel folding pattern for a serine protein kinase. J Biol Chem. 2001 Oct 5;276(40):37443-50. DOI:10.1074/jbc.M104285200 |

Other References

1. Izquierdo pmid=17135269