Alternative titles; symbols
HGNC Approved Gene Symbol: PSMD4
Cytogenetic location: 1q21.3 Genomic coordinates (GRCh38): 1:151,254,734-151,267,479 (from NCBI)
Ubiquitination targets proteins for degradation by the 26S proteasome. The 26S proteasome contains a 20S catalytic core particle (see 602175) capped at either or both ends by 19S regulatory particles, which prepare substrates for hydrolysis in the core region. PSMD4 is a component of the regulatory particle that functions as a polyubiquitin receptor and captures substrates by recognizing their covalently attached ubiquitin chains (Zhang et al., 2009).
Deveraux et al. (1994) identified a 50-kD subunit of the regulatory complex of the 26S proteasome. They called this protein subunit-5 (S5) based upon its relative mobility on SDS-polyacrylamide gels. Deveraux et al. (1994) demonstrated that 2 distinct subunits of the 26S protease migrate as 50-kD proteins, and thus, S5 represents 2 proteins, which the authors termed S5A, also called PSMD4, and S5B (PSMD5; 604452). PSMD4 focuses at pH 4.6 on 2-dimensional gels.
Ferrell et al. (1996) cloned a HeLa cell cDNA encoding S5A using cDNA probes based upon the sequence of Mbp1, an Arabidopsis protein physically, immunologically, and biochemically similar to S5A. The HeLa cell-derived cDNA sequence is highly similar to Mbp1 and encodes polypeptides obtained directly from human erythrocyte S5A. Expression of recombinant S5A in E. coli resulted in a protein with an apparent molecular mass matching that of the purified S5A subunit. The deduced 378-amino acid protein has a calculated molecular mass of 40.3 kD. S5A has several domains that are highly conserved between Arabidopsis, Drosophila, and Saccharomyces orthologs. A conserved 190-amino acid N-terminal domain is followed by a conserved glycine-rich region, a conserved C-terminal half containing repeated sequences, and a C terminus rich in lysine and glutamate residues (KEKE region).
Using deletion analysis, Young et al. (1998) identified 2 conserved polyubiquitin-binding sites in the C-terminal half of human S5A. These sites, which the authors called PUbS1 and PUbS2, are about 30 amino acids long and are separated by a 50-amino acid linker.
By PCR of an adult mouse testis cDNA library, Kawahara et al. (2000) cloned mouse Rpn10a, which encodes a protein 95% identical to human S5A. They cloned 4 other variants of mouse Rpn10, Rpn10b through Rpn10e, by PCR of embryos and embryonic stem cells. The 5 Rpn10 variants differ in the splicing of their last 4 exons, exons 7 through 10. The deduced proteins are identical in their N-terminal halves, including the PUbS1, but differ in their C-terminal halves by the presence or absence of a short insertion between PUbS1 and PUbS2 and by various C-terminal truncations. Only Rpn10a and Rpn10b contain the C-terminal KEKE region. The shortest mouse isoform, Rpn10e, is truncated following PUbS1. Kawahara et al. (2000) cloned human RPN10e by PCR of a human fetal brain cDNA library. RT-PCR detected ubiquitous expression of mouse Rpn10a, whereas Rpn10e was expressed exclusively in mouse embryos, with highest expression in embryonic brain.
Deveraux et al. (1994) found that S5 bound ubiquitinated lysozyme as well as free polymers of ubiquitin. S5 efficiently bound to tetrameric ubiquitin and selected for longer ubiquitin polymers, a property consistent with characteristics expected of a component that selects ubiquitin conjugates for proteolysis. Deveraux et al. (1994) showed that S5A bound to ubiquitin polymers in vitro, whereas S5B did not.
Ferrell et al. (1996) found that recombinant human S5A bound multiubiquitin chains in a manner similar to that shown by the endogenous erythrocyte proteasome regulatory complex.
Using deletion analysis, Young et al. (1998) found that PUbS1 and PUbS2 were required to bind ubiquitin. PUbS1 and PUbS2 differed by at least 10-fold in their apparent affinity for ubiquitin trimers and tetramers, and in full-length S5A, they appeared to bind polyubiquitin chains in a cooperative manner. Full-length S5A inhibited ubiquitin-lysozyme conjugate degradation in rabbit reticulocyte lysates.
Kawahara et al. (2000) identified mouse Rpn10e as a component of an embryo-specific proteasome. Both mouse Rpn10a and Rpn10e bound multiubiquitinated lysozyme with similar affinities in vitro, and they inhibited degradation of multiubiquitinated lysozyme by the proteasome with similar efficiency. However, unlike Rpn10a, Rpn10e was unable to inhibit degradation of cyclin B2 (CCNB2; 602755) in Xenopus egg extracts.
Husnjak et al. (2008) reported the identification of Rpn13/ARM1 (ADRM1; 610650), a component of the proteasome, as a ubiquitin receptor. Like proteasomal ubiquitin receptor Rpn10/S5a, Rpn13 also binds ubiquitin-like domains of ubiquitin-like ubiquitin-associated proteins. In yeast, a synthetic phenotype results when specific mutations of the ubiquitin binding sites of Rpn10 and Rpn13 are combined, indicating functional linkage between these ubiquitin receptors. Because Rpn13 is also the proteasomal receptor for Uch37 (610667), a deubiquitinating enzyme, Husnjak et al. (2008) concluded that their findings suggested a coupling of chain recognition and disassembly at the proteasome.
Using nuclear magnetic resonance and analytical ultracentrifugation, Zhang et al. (2009) characterized binding between the isolated ubiquitin-interacting motifs (UIMs) of S5A and lys48 (K48)-linked diubiquitin, in which K48 of the proximal ubiquitin subunit was covalently bound to gly76 (G76) of the distal subunit. The UIMs of S5A bound diubiquitin simultaneously, with a preference for UIM2 binding the proximal subunit and UIM1 binding the distal subunit. The coordinated binding of both UIMs to diubiquitin showed higher affinity than binding of either UIM to monoubiquitin. S5A and RPN13 could bind a common diubiquitin chain. In these complexes, RPN13 preferentially bound the proximal subunit, and the 2 UIMs of S5A competed for the distal subunit. Since the 2 UIMs of S5A preferentially bound separate ubiquitin subunits in diubiquitin in the absence of RPN13, that authors suggested that the UIMs of S5A would likely occupy separate ubiquitin subunits in longer ubiquitin chains.
Hartz (2009) mapped the PSMD4 gene to chromosome 1q21.3 based on an alignment of the PSMD4 sequence (GenBank U24704) with the genomic sequence (GRCh37).
Kawahara et al. (2000) mapped the mouse Psmd4 gene to chromosome 3.
Deveraux, Q., Jensen, C., Rechsteiner, M. Molecular cloning and expression of a 26 S protease subunit enriched in dileucine repeats. J. Biol. Chem. 270: 23726-23729, 1995. [PubMed: 7559544] [Full Text: https://doi.org/10.1074/jbc.270.40.23726]
Deveraux, Q., Ustrell, V., Pickart, C., Rechsteiner, M. A 26 S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269: 7059-7061, 1994. [PubMed: 8125911]
Ferrell, K., Deveraux, Q., van Nocker, S., Rechsteiner, M. Molecular cloning and expression of a multiubiquitin chain binding subunit of the human 26S protease. FEBS Lett. 381: 143-148, 1996. [PubMed: 8641424] [Full Text: https://doi.org/10.1016/0014-5793(96)00101-9]
Hartz, P. A. Personal Communication. Baltimore, Md. 10/5/2009.
Husnjak, K., Elsasser, S., Zhang, N., Chen, X., Randles, L., Shi, Y., Hofmann, K., Walters, K. J., Finley, D., Dikic, I. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453: 481-488, 2008. [PubMed: 18497817] [Full Text: https://doi.org/10.1038/nature06926]
Kawahara, H., Kasahara, M., Nishiyama, A., Ohsumi, K., Goto, T., Kishimoto, T., Saeki, Y., Yokosawa, H., Shimbara, N., Murata, S., Chiba, T., Suzuki, K., Tanaka, K. Developmentally regulated, alternative splicing of the Rpn10 gene generates multiple forms of 26S proteasomes. EMBO J. 19: 4144-4153, 2000. [PubMed: 10921894] [Full Text: https://doi.org/10.1093/emboj/19.15.4144]
Young, P., Deveraux, Q., Beal, R. E., Pickart, C. M., Rechsteiner, M. Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a. J. Biol. Chem. 273: 5461-5467, 1998. [PubMed: 9488668] [Full Text: https://doi.org/10.1074/jbc.273.10.5461]
Zhang, N., Wang, Q., Ehlinger, A., Randles, L., Lary, J. W., Kang, Y., Haririnia, A., Storaska, A. J., Cole, J. L., Fushman, D., Walters, K. J. Structure of the S5a:K48-linked diubiquitin complex and its interactions with Rpn13. Molec. Cell 35: 280-290, 2009. [PubMed: 19683493] [Full Text: https://doi.org/10.1016/j.molcel.2009.06.010]