Alternative titles; symbols
HGNC Approved Gene Symbol: IPPK
Cytogenetic location: 9q22.31 Genomic coordinates (GRCh38): 9:92,613,183-92,670,131 (from NCBI)
IPPK catalyzes phosphorylation of inositol 1,3,4,5,6-pentakisphosphate (IP5) to generate inositol hexakisphosphate (IP6) (Verbsky et al., 2002). IPPK also plays a noncatalytic role in the synthesis of ribosomal RNA (rRNA) by functioning as a molecular scaffold in nucleoli (Brehm et al., 2013).
Verbsky et al. (2002) cloned human IPPK, which they called InsP5 2-kinase, from a spleen cDNA library. The predicted IPPK protein contains 491 amino acids. Northern blot analysis showed that IPPK was ubiquitously expressed in human tissues, with high levels in heart, brain, testis, and placenta.
Using immunofluorescence analysis, Brehm et al. (2013) showed that IPPK, which they termed IP5K, localized throughout nuclei of human cells, including in nucleoli.
Gross (2020) mapped the IPPK gene to chromosome 9q22.31 based on an alignment of the IPPK sequence (GenBank AF351202) with the genomic sequence (GRCh38).
Verbsky et al. (2002) confirmed that recombinant human IPPK catalyzed the synthesis of InsP6 and determined its kinetic features.
Using in situ hybridization, Sarmah et al. (2005) showed that zebrafish ippk, which they termed ipk1, was expressed symmetrically during gastrulation and early segmentation in embryogenesis. Knockdown of ipk1 altered inositol polyphosphate levels and resulted in concordant randomization of both molecular and morphologic asymmetries in zebrafish embryos. Moreover, loss of ipk1 eliminated the normal left-biased intracellular Ca(2+) flux in cells surrounding Kupffer vesicle, an organ implicated in early steps of left-right patterning.
Using immunoprecipitation analysis, Brehm et al. (2013) showed that IP5K interacted with TCOF1 (606847), UBF (UBTF; 600673), and CK2 (see 115440), all of which regulate rRNA synthesis. Molecular modeling and mutagenic studies showed that an RKK tripeptide in IP5K mediated its interaction with UBF. The spatial organization of nucleolar IP5K was sensitive to inhibition of rRNA synthesis. Further analyses showed that IP5K played a noncatalytic role in regulating the spatial distributions of UBF, TCOF1, and Pol I (see 616404) by functioning as a molecular scaffold, thereby contributing to nucleolar architecture in intact cells and influencing the degree of rRNA synthesis.
Scherer et al. (2016) showed that IP5K bound to cullin-RING E3 ubiquitin ligases (CRLs) by interacting with cullins (e.g., CUL1; 603134). IP6 generated by IP5K increased affinity between cullins and CSN2 (COPS2; 604508), a subunit of the COP9 signalosome (CSN). The findings indicated that IP5K regulates CRL downstream functions by facilitating assembly of CRL-CSN complexes and switching CRLs from their active state to inactive state.
Using limited proteolysis, Gosein and Miller (2013) showed that N-lobe stability of IPPK, which they called IPK1, was dependent on the presence of 1-phosphate group in IPs. However, overall stability of IPK1 was increased in ternary complexes with nucleotide and IPs, when IP binding sites in the N-lobe were occupied by the 1- and 3-phosphate groups of the IPs. The findings indicated that the 1- and 3-phosphates of substrates possessed dual roles in both IPK1 activation and IPK1 stability. Artificial introduction of a disulfide bond through mutation in IPK1 diminished the requirement for N-lobe-interacting 1- and 3-phosphates and stabilized IPK1 in an IP-independent manner, thereby mimicking its substrate-bound state in the absence of IP. Crystal structure of the mutant confirmed formation of a disulfide bond and revealed a shift of the N-lobe in the mutant structure compared with the wildtype structure. The presence of the disulfide bond increased the overall stability of IPK1 and altered its substrate specificity, as the mutant IPK1 recognized substrates lacking the 1-phosphate, indicating that N-lobe stability was a determinant of IPK1 substrate specificity.
Franco-Echevarria et al. (2017) determined the crystal structure of mouse Ippk at 2.4-angstrom resolution from a truncated Ippk lacking 21 C-terminal residues in complex with 1 or both ligands, forming binary complexes (IP6) or ternary complexes (IP5/ATP). The Ippk structure contained N- and C-terminal lobes connected by a hinge, with both lobes coordinating a nucleotide between them. A helical scaffold in the C-lobe constituted the IP-binding site, which, along with participation of the N-lobe, endowed high specificity to the protein. The authors also identified a basic patch on the surface of the enzyme that functioned as a zinc-binding site. Comparison with the structure of Ippk from Arabidopsis thaliana revealed unexpected protein regions and residues in mouse Ippk.
Brehm, M. A., Wundenberg, T., Williams, J., Mayr, G. W., Shears, S. B. A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA. J. Cell Sci 126: 437-444, 2013. [PubMed: 23203802] [Full Text: https://doi.org/10.1242/jcs.110031]
Franco-Echevarria, E., Sanz-Aparicio, J., Brearley, C. A., Gonzalez-Rubio, J. M., Gonzalez, B. The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function. J. Biol. Chem. 292: 10534-10548, 2017. [PubMed: 28450399] [Full Text: https://doi.org/10.1074/jbc.M117.780395]
Gosein, V., Miller, G. J. Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity. J. Biol. Chem. 288: 36788-36795, 2013. [PubMed: 24165122] [Full Text: https://doi.org/10.1074/jbc.M113.512731]
Gross, M. B. Personal Communication. Baltimore, Md. 10/7/2020.
Sarmah, B., Latimer, A. J., Appel, B., Wente, S. R. Inositol polyphosphates regulate zebrafish left-right asymmetry. Dev. Cell 9: 133-145, 2005. [PubMed: 15992547] [Full Text: https://doi.org/10.1016/j.devcel.2005.05.002]
Scherer, P. C., Ding, Y., Liu, Z., Xu, J., Mao, H.,, Barrow, J. C., Wei, N.,, Zheng, N., Snyder, S. H., Rao, F. Inositol hexakisphosphate (IP6) generated by IP5K mediates cullin-COP9 signalosome interactions and CRL function. Proc. Nat. Acad. Sci. 113: 3503-3508, 2016. [PubMed: 26976604] [Full Text: https://doi.org/10.1073/pnas.1525580113]
Verbsky, J. W., Wilson, M. P., Kisseleva, M. V., Majerus, P. W., Wente, S. R. The synthesis of inositol hexakisphosphate: characterization of human inositol 1,3,4,5,6-pentakisphosphate 2-kinase. J. Biol. Chem. 277: 31857-31862, 2002. [PubMed: 12084730] [Full Text: https://doi.org/10.1074/jbc.M205682200]