About

Steven G. Clarke is a professor whose lab at UCLA focuses on the role of methylation and its associated enzymes in aging and disease states. He has been featured in an episode of Let's Talk Chemistry, highlighting his contributions to the field. His research emphasizes understanding the biochemical mechanisms underlying methylation processes and their implications for health and disease.

Research topics

• Biochemistry
• Biology
• Chemistry
• Cell biology
• Molecular biology

Selected publications

• PRMT7 as a unique member of the protein arginine methyltransferase family: A review

  UNC Libraries · 2026-04-11

  articleOpen access1st authorCorresponding
  PublisherDOI

• Structural basis for L-isoaspartyl-containing protein recognition by the human PCMTD1 cullin-RING E3 ubiquitin ligase

  Journal of Biological Chemistry · 2025-09-19 · 1 citations

  articleOpen accessSenior author

  A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining proteome stability and prolonging organismal survival. Although repair through methylation by PCMT1 has been previously shown to suppress L-isoaspartyl accumulation, we provide an additional mechanism for L-isoaspartyl maintenance through PCMTD1, a cullin-RING ligase (CRL). We combined cryo-EM, native mass spectrometry, and biochemical assays to provide insight on how the assembly and architecture of human PCMTD1 in the context of a CRL complex fulfills this alternative mechanism. We show that the PCMTD1 CRL complex specifically binds L-isoaspartyl residues when bound to AdoMet. This work provides evidence for a growing class of E3 ubiquitin ligases that recognizes spontaneous covalent modifications as potential substrates for ubiquitylation and subsequent proteasomal degradation.

  PublisherDOI

• Abstract 2641 An enzymology approach to understanding CoQ deficiency: unraveling the structure-function relationship of COQ5

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access

  Coenzyme Q (CoQ) is an essential lipid that functions as an electron carrier in the mitochondrial electron transport chain. In its reduced form (CoQH2), it can also act as a chain-terminating antioxidant providing protection against lipid peroxidation and ferroptosis. Genetic defects in the CoQ biosynthetic pathway in humans can cause a wide array of illnesses, including cardiovascular, kidney, and neurodegenerative disorders, through a condition known as primary CoQ deficiency. We focus on COQ5, a gene encoding an S-adenosylmethionine (AdoMet)-dependent C-methyltransferase in the CoQ biosynthetic pathway.

  PublisherOA PDFDOI

• List of contributors

  Handbook of Proteolytic Enzymes · 2025-01-01

  book-chapter
  PublisherDOI

• Structural basis for L-isoaspartyl-containing protein recognition by the PCMTD1 cullin-RING E3 ubiquitin ligase

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-21 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Summary A major type of spontaneous protein damage that accumulates with age is the formation of kinked polypeptide chains with L-isoaspartyl residues. Mitigating this damage is necessary for maintaining proteome stability and prolonging organismal survival. While repair through methylation by PCMT1 has been previously shown to suppress L-isoaspartyl accumulation, we provide an additional mechanism for L-isoaspartyl maintenance through PCMTD1, a cullin-RING ligase (CRL). We combined cryo-EM, native mass spectrometry, and biochemical assays to provide insight on how the assembly and architecture of PCMTD1 in the context of a CRL complex fulfils this alternative mechanism. We show that the PCMTD1 CRL complex specifically binds L-isoaspartyl residues when bound to AdoMet. This work provides evidence for a growing class of E3 ubiquitin ligases that recognize spontaneous covalent modifications as potential substrates for ubiquitylation and subsequent proteasomal degradation. eTOC Blurb Limiting the accrual of L-isoaspartyl damaged proteins is essential during aging. While this is thought to be mediated solely by the repair activity of the protein, PCMT1, Pang et al. now demonstrate that a related protein, PCMTD1, functions as a cullin-RING ligase to selectively target L-isoaspartyl-damaged substrates for potential regulation by the ubiquitylation-proteosomal system. Highlights Atomic cryo-EM structure of CRL5-PCMTD1 determined Architecture of PCMTD1 when complexed as a CRL supports ubiquitylation activity PCMTD1 recognizes L-isoaspartyl residues as a recruitment motif for potential CRL activity Recognition of L-isoaspartyl residues is dependent on cofactor engagement

  PublisherOA PDFDOI

• Isoaspartyl dipeptidase (IadA)

  Handbook of Proteolytic Enzymes · 2025-01-01

  book-chapterSenior author
  PublisherDOI

• The Function and Enzymology of Protein d-Aspartyl/l-Isoaspartyl Methyltransferases in Eukaryotic and Prokaryotic Cells

  2024-12-12 · 1 citations

  book-chapterSenior author

  Enzymes that catalyze the incorporation of methyl groups from S-adenosylmethionine into protein carboxyl groups have been found widely distributed in nature. 1 , 2 At this point, there appear to be three major classes of these protein methyltransferases that can be classified according to their methyl-acceptor specificity. One of these (type I) catalyzes the formation of glutamyl side chain methyl esters 3 , 4 from a set of specific l-glutamic acid residues on the receptors of chemotactic bacteria. 5 , 6 This glutamyl methyltransferase functions in the modulation of the output of these chemoreceptors. 7 The second class (type II) is much more widely distributed in both eukaryotic and prokaryotic cells and appears to methylate carboxyl groups on atypical amino acid residues which can be derived from both aspartyl and asparaginyl residues. These abnormal groups include d-aspartyl 8 and l-isoaspartyl residues. 9 , 10 No methyldonor activity has been observed with this enzyme on substrates containing only normal l-aspartyl (or l-glutamyl) residues. The role of the type II enzyme appears to be in the recognition and methylation of abnormal or damaged proteins in the cell for possible repair or degradation reactions. 8–14 Finally, the existence of a third class of enzymes (type III) that appears to modify the alpha carboxyl group of the C-terminal cysteine residue of various membrane-related proteins has been inferred from the presence of methylated peptidyl yeast sex factors 15 , 16 and experimental evidence has been presented for such methylation of the mammalian ras oncogene products,16a,16b and other proteins. The differences between these three classes of enzymes are summarized in Table 1. The work in our laboratory has focused on the type II d-aspartyl/l-isoaspartyl methyltransferase, and we will concentrate on this enzyme in this review.

  PublisherDOI

• Genetic Risk of Reticular Pseudodrusen in Age-Related Macular Degeneration: <i>HTRA1</i> /lncRNA <i>BX842242.1</i> dominates, with no evidence for Complement Cascade involvement

  medRxiv · 2024-09-28 · 6 citations

  preprintOpen access

  Abstract Age-related macular degeneration (AMD) is a multifactorial retinal disease with a large genetic risk contribution. Reticular pseudodrusen (RPD) is a sub-phenotype of AMD with a high risk of progression to late vision threatening AMD. In a genome-wide association study of 2,165 AMD+/RPD+ and 4,181 AMD+/RPD-compared to 7,660 control participants, both chromosomes 1 ( CFH ) and 10 ( ARMS2/HTRA1 ) major AMD risk loci were reidentified. However association was only detected for the chromosome 10 locus when comparing AMD+/RPD+ to AMD+/RPD-cases. The chromosome 1 locus was notably absent. The chromosome 10 RPD risk region contains a long non-coding RNA (ENSG00000285955/BX842242.1) which colocalizes with genetic markers of retinal thickness. BX842242.1 has a strong retinal eQTL signal, pinpointing the parafoveal photoreceptor outer segment layer. Whole genome sequencing of phenotypically extreme RPD cases identified even stronger enrichment for the chromosome 10 risk genotype.

  PublisherOA PDFDOI

• Methylation and phosphorylation of formin homology domain proteins (Fhod1 and Fhod3) by protein arginine methyltransferase 7 (PRMT7) and Rho kinase (ROCK1)

  Journal of Biological Chemistry · 2024-10-04 · 1 citations

  articleOpen accessSenior author

  Protein post-translational modifications (PTMs) can regulate biological processes by altering an amino acid's bulkiness, charge, and hydrogen bonding interactions. Common modifications include phosphorylation, methylation, acetylation, and ubiquitylation. Although a primary focus of studying PTMs is understanding the effects of a single amino acid modification, the possibility of additional modifications increases the complexity. For example, substrate recognition motifs for arginine methyltransferases and some serine/threonine kinases overlap, leading to potential enzymatic crosstalk. In this study we have shown that the human family of formin homology domain-containing proteins (Fhods) contain a substrate recognition motif specific for human protein arginine methyltransferase 7 (PRMT7). In particular, PRMT7 methylates two arginine residues in the diaphanous autoinhibitory domain (DAD) of the family of Fhod proteins: R1588 and/or R1590 of Fhod3 isoform 4. Additionally, we confirmed that S1589 and S1595 in the DAD domain of Fhod3 can be phosphorylated by Rho/ROCK1 kinase. Significantly, we have determined that if S1589 is phosphorylated then PRMT7 cannot subsequently methylate R1588 or R1590. In contrast, if R1588 or R1590 of Fhod3 is methylated then ROCK1 phosphorylation activity is only slightly affected. Finally, we show that the interaction of the N-terminal DID domain can also inhibit the methylation of the DAD domain. Taken together these results suggest that the family of Fhod proteins, potential in vivo substrates for PRMT7, might be regulated by a combination of methylation and phosphorylation.

  PublisherDOI

• The exquisite specificity of human protein arginine methyltransferase 7 (PRMT7) toward Arg-X-Arg sites

  PLoS ONE · 2023-05-22 · 4 citations

  articleOpen accessSenior authorCorresponding

  Mammalian protein arginine methyltransferase 7 (PRMT7) has been shown to target substrates with motifs containing two arginine residues separated by one other residue (RXR motifs). In particular, the repression domain of human histone H2B (29-RKRSR-33) has been a key substrate in determining PRMT7 activity. We show that incubating human PRMT7 and [3H]-AdoMet with full-length Xenopus laevis histone H2B, containing the substitutions K30R and R31K (RKRSR to RRKSR), results in greatly reduced methylation activity. Using synthetic peptides, we have now focused on the enzymology behind this specificity. We show for the human and Xenopus peptide sequences 23-37 the difference in activity results from changes in the Vmax rather than the apparent binding affinity of the enzyme for the substrates. We then characterized six additional peptides containing a single arginine or a pair of arginine residues flanked by glycine and lysine residues. We have corroborated previous findings that peptides with an RXR motif have much higher activity than peptides that contain only one Arg residue. We show that these peptides have similar apparent km values but significant differences in their Vmax values. Finally, we have examined the effect of ionic strength on these peptides. We found the inclusion of salt had little effect on the Vmax value but a considerable increase in the apparent km value, suggesting that the inhibitory effect of ionic strength on PRMT7 activity occurs largely by decreasing apparent substrate-enzyme binding affinity. In summary, we find that even subtle substitutions in the RXR recognition motif can dramatically affect PRMT7 catalysis.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R01AG018000

  NIH · $904k · 2005

• Role of Protein Methylation in Translation

  NSF · $800k · 2017–2023

• NIH Grant R01GM026020

  NIH · $6.2M · 2016

• Collaborative Research: Maintenance of a Functional Proteome through Dynamic Repair

  NSF · $149k · 2005–2009

• Research Tranining in Cellular and Molecular Biology

  NIH · $29.3M · 1975–2021

Frequent coauthors

• Jonathan D. Lowenson

  University of California, Los Angeles

  40 shared

• Joyce Sayegh

  Yale University

  33 shared

• Robert G. Roeder

  Rockefeller University

  25 shared

• Julie R. Perlin

  Howard Hughes Medical Institute

  25 shared

• Richard G. Cook

  University of Tennessee at Chattanooga

  25 shared

• Charles H. McDonald

  Baylor College of Medicine

  25 shared

• Lakshmi S. Sonbuchner

  Cornell University

  25 shared

• Lauriebeth Leonelli

  University of Illinois Urbana-Champaign

  25 shared