Crystal Structure and Functional Analysis of JMJD5 Indicate an Alternate Specificity and Function

Abstract

JMJD5 is a Jumonji C (JmjC) protein that has been implicated in breast cancer tumorigenesis, circadian rhythm regulation, embryological development, and osteoclastogenesis. Recently, JMJD5 (also called KDM8) has been reported to demethylate dimethylated Lys-36 in histone H3 (H3K36me2), regulating genes that control cell cycle progression. Here, we report high-resolution crystal structures of the human JMJD5 catalytic domain in complex with the substrate 2-oxoglutarate (2-OG) and the inhibitor N-oxalylglycine (NOG). The structures reveal a ␤-barrel fold that is conserved in the JmjC family and a long shallow cleft that opens into the enzyme's active site. A comparison with other JmjC enzymes illustrates that JMJD5 shares sequence and structural homology with the asparaginyl and histidinyl hydroxylase FIH-1 (factor inhibiting hypoxia-inducible factor 1 [HIF-1]), the lysyl hydroxylase JMJD6, and the RNA hydroxylase TYW5 but displays limited homology to JmjC lysine demethylases (KDMs). Contrary to previous findings, biochemical assays indicate that JMJD5 does not display demethylase activity toward methylated H3K36 nor toward the other methyllysines in the N-terminal tails of histones H3 and H4. Together, these results imply that JMJD5 participates in roles independent of histone demethylation and may function as a protein hydroxylase given its structural homology with FIH-1 and JMJD6.T he Jumonji C (JmjC) enzymes represent a family of nonheme Fe(II)-and 2-oxoglutarate (2-OG)-dependent dioxygenases (5, 12). These enzymes belong to the Cupin protein superfamily whose members share a conserved ␤-barrel fold and possess a His-X-Glu/Asp-X n -His triad responsible for Fe(II) coordination (11,20,33,40). Metazoan JmjC proteins comprise several subfamilies that possess distinct substrate specificities and participate in different biological processes, including transcriptional regulation, cell cycle control, chromatin modification, mRNA splicing, and RNA modification (13,35,37,43,50). Enzymes from several of the JmjC subfamilies have been shown to function as lysine demethylases (KDMs) by hydroxylating the methyl groups of methyllysines in histones and nonhistone proteins. These subfamilies include JHDM1 (KDM2), JHDM2 (KDM3), JMJD2 (KDM4), JARID1, (KDM5), UTX/JMJD3 (KDM6), and PHF8/ KIAA1718 (KDM7) (2,22,35,45). In contrast, other JmjC enzymes catalyze stereo-and site-specific hydroxylation of residues in nonhistone proteins. Examples of these enzymes include JMJD6, a lysyl-5S-hydroxylase that oxidizes the splicing factor U2AF65 (32, 50), and FIH-1 (factor inhibiting hypoxia-inducible factor 1 [HIF-1]), an asparaginyl, aspartyl, and histidinyl hydroxylase whose substrates include the HIF and ankyrin repeat-containing proteins (13, 43, 51, 52). Moreover, recent studies have highlighted that JmjC substrates are not restricted to proteins. The tRNA wybutosine-synthesizing enzyme 5 (TYW5) hydroxylates wybutosine to hydroxywybutosine at position 37 in phenylalanine tRNA, illustrating that certain JmjC enzymes can oxidize nucleic...

Hepatocyte Factor JMJD5 Regulates Hepatitis B Virus Replication through Interaction with HBx

“…These results suggest that both the association of JMJD5 with HBx and the hydroxylase activity in JMJD5 are required for efficient replication of HBV. JMJD6, which has a JmjC domain structurally similar to that of JMJD5 (36,38), possesses lysyl-hydroxylase activity and catalyzes the U2 small nuclear ribonucleoprotein auxiliary factor 65-kDa subunit (U2AF65) to regulate RNA splicing (75) and hydroxylation of lysine residues in histone (76,77). Further studies are needed to identify the molecular targets of JMJD5 in hepatocytes.…”

“…Structural analyses have shown that JMJD5 exhibits hydroxylase activity rather than demethylase activity (36,37). The structure of the jumonji C domain of JMJD5 was conserved with the C-terminal transactivation domains of the factor inhibiting hypoxia-inducible 1 alpha (FIH-1) and JMJD6 (36,38). The C-terminal transactivation domain of FIH-1 exhibits an asparaginyl hydroxylase activity to catalyze hydroxylation of Asp 803 of hypoxia-inducible factor (39).…”

Clipping of arginine-methylated histone tails by JMJD5 and JMJD7

“…The exact functions of JMJD5 remain controversial. JMJD5 has been suggested to possess H3K36 lysine demethylase (21) and/or a hydroxylase activities (22,23). The possibility remains that JMJD5 and some other "orphan" JmjC proteins target methyl arginines in histones and/or other proteins via different mechanisms.…”

JMJD5 (Jumonji Domain-containing 5) Associates with Spindle Microtubules and Is Required for Proper Mitosis

“…JMJD5 was reported to be histone H3K36me2 demethylase and non-histone protein hydroxylase (13,16). The crystal structure of JMJD5 showed that, in the catalytic site, Fe 2ϩ could be chelated by residues His 321 , Asp 323 , and His 400 (27,28). This HX(D/E)X n H motif is highly conserved in JmjC domain-containing proteins and is important for their catalytic activity (29).…”