Experts and Doctors on substrate specificity in Bethesda, Maryland, United States


Locale: Bethesda, Maryland, United States
Topic: substrate specificity

Top Publications

  1. Datta K, Weinfeld M, Neumann R, Winters T. Determination and analysis of site-specific 125I decay-induced DNA double-strand break end-group structures. Radiat Res. 2007;167:152-66 pubmed
    ..Even so, end-group structure and relative distribution varied as a function of the free radical scavenging capacity of the irradiation buffer. ..
  2. Xia D, Esser L, Tang W, Zhou F, Zhou Y, Yu L, et al. Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. Biochim Biophys Acta. 2013;1827:1278-94 pubmed publisher
    ..This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes. ..
  3. Zhi L, Mans J, Paskow M, Brown P, Schuck P, Jonjić S, et al. Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms. Biochemistry. 2010;49:2443-53 pubmed publisher
    ..Molecular modeling of the different RAE-1 isoforms suggests a potential site for the m152 interaction. ..
  4. Revoredo L, Wang S, Bennett E, Clausen H, Moremen K, Jarvis D, et al. Mucin-type O-glycosylation is controlled by short- and long-range glycopeptide substrate recognition that varies among members of the polypeptide GalNAc transferase family. Glycobiology. 2016;26:360-76 pubmed publisher
    ..These studies further demonstrate that both domains of the ppGalNAc-Ts have specialized and unique functions that work in concert to control and order mucin-type O-glycosylation. ..
  5. Chattopadhyay M, Tabor C, Tabor H. Spermidine but not spermine is essential for hypusine biosynthesis and growth in Saccharomyces cerevisiae: spermine is converted to spermidine in vivo by the FMS1-amine oxidase. Proc Natl Acad Sci U S A. 2003;100:13869-74 pubmed
    ..We have also shown this conversion in enzymatic studies by using the purified amine oxidase from yeast. ..
  6. Sundaram A, Pitts L, Muhammad K, Wu J, Betenbaugh M, Woodard R, et al. Characterization of N-acetylneuraminic acid synthase isoenzyme 1 from Campylobacter jejuni. Biochem J. 2004;383:83-9 pubmed
    ..The present study is the first stereochemical analysis of the reaction catalysed by a bacterial NeuNAc synthase. ..
  7. Sannerud R, Esselens C, Ejsmont P, Mattera R, Rochin L, Tharkeshwar A, et al. Restricted Location of PSEN2/?-Secretase Determines Substrate Specificity and Generates an Intracellular A? Pool. Cell. 2016;166:193-208 pubmed publisher
    ..The findings reveal potentially important roles for specific intracellular, localized reactions contributing to AD pathogenesis. ..
  8. Li W, Zhang J, Bottaro D, Pierce J. Identification of serine 643 of protein kinase C-delta as an important autophosphorylation site for its enzymatic activity. J Biol Chem. 1997;272:24550-5 pubmed
    ..Taken together, our results demonstrate that serine 643 of PKC-delta is a major autophosphorylation site, and phosphorylation of this site plays an important role in controlling its enzymatic activity and biological function. ..
  9. Maruoka H, Barrett M, Ko H, Tosh D, Melman A, Burianek L, et al. Pyrimidine ribonucleotides with enhanced selectivity as P2Y(6) receptor agonists: novel 4-alkyloxyimino, (S)-methanocarba, and 5'-triphosphate gamma-ester modifications. J Med Chem. 2010;53:4488-501 pubmed publisher
    ..47 and 0.18 microM, respectively). Thus, the potency, selectivity, and stability of pyrimidine nucleotides as P2Y(6) receptor agonists may be enhanced by modest structural changes. ..

More Information


  1. Kohjitani A, Fuda H, Hanyu O, Strott C. Cloning, characterization and tissue expression of rat SULT2B1a and SULT2B1b steroid/sterol sulfotransferase isoforms: divergence of the rat SULT2B1 gene structure from orthologous human and mouse genes. Gene. 2006;367:66-73 pubmed
    ..Furthermore, unlike the case with human and mouse SULT2B1 genes where differential splicing is necessitated since a portion of exon IA is fused with exon IB to complete the SULT2B1b mRNA, this step is not required with the rat gene. ..
  2. Randazzo P, Inoue H, Bharti S. Arf GAPs as regulators of the actin cytoskeleton. Biol Cell. 2007;99:583-600 pubmed
    ..With multiple functional elements, the Arf GAPs could integrate signals and biochemical activities that result in co-ordinated changes in actin and membranes necessary for a wide range of cellular functions. ..
  3. Sidorova N, Muradymov S, Rau D. Solution parameters modulating DNA binding specificity of the restriction endonuclease EcoRV. FEBS J. 2011;278:2713-27 pubmed publisher
    ..In addition to divalent ions, water activity and pH are key parameters that strongly modulate binding specificity of EcoRV. ..
  4. Sadrieh N, Snyderwine E. Cytochromes P450 in cynomolgus monkeys mutagenically activate 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) but not 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx). Carcinogenesis. 1995;16:1549-55 pubmed
    ..Furthermore, the poor metabolic activation of MeIQx by CYP3A and CYP2C, coupled with low constitutive levels of CYP1A isozymes, provide a metabolic explanation for the low hepatocarcinogenic potency of MeIQx in cynomolgus monkeys...
  5. Thomas J, Moos M. Vg1 has specific processing requirements that restrict its action to body axis patterning centers. Dev Biol. 2007;310:129-39 pubmed
    ..Taken together, these observations provide a plausible mechanism for local action of Vg1 consistent with requirements imposed by current models of pattern formation in the developing body axis. ..
  6. Lim J, You Z, Kim G, Levine R. Methionine sulfoxide reductase A is a stereospecific methionine oxidase. Proc Natl Acad Sci U S A. 2011;108:10472-7 pubmed publisher
    ..MsrA catalyzes its own autooxidation as well as oxidation of free methionine and methionine residues in peptides and proteins. When functioning as a reductase, MsrA fully reverses the oxidations which it catalyzes. ..
  7. Hollingsworth H, Nossal N. Bacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro. J Biol Chem. 1991;266:1888-97 pubmed
    ..Addition of T4 RNase H and T4 DNA ligase leads to extensive joining of discontinuous lagging strand fragments in the T4 DNA replication system in vitro. ..
  8. Noguchi M, Sarin A, Aman M, Nakajima H, Shores E, Henkart P, et al. Functional cleavage of the common cytokine receptor gamma chain (gammac) by calpain. Proc Natl Acad Sci U S A. 1997;94:11534-9 pubmed
    ..Together, these data suggest that calpain-mediated cleavage of gammac represents a mechanism by which gammac-dependent signaling can be controlled. ..
  9. Galperin M, Moroz O, Wilson K, Murzin A. House cleaning, a part of good housekeeping. Mol Microbiol. 2006;59:5-19 pubmed
    ..We discuss the structural diversity of these enzymes, their phylogenetic distribution, substrate specificity and the problem of identifying their true substrates. ..
  10. Nowotny M, Gaidamakov S, Ghirlando R, Cerritelli S, Crouch R, Yang W. Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol Cell. 2007;28:264-76 pubmed
    ..The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors. ..
  11. Quan Q, Yang M, Gao H, Zhu L, Lin X, Guo N, et al. Imaging tumor endothelial marker 8 using an 18F-labeled peptide. Eur J Nucl Med Mol Imaging. 2011;38:1806-15 pubmed publisher
    ..18F-FP-QQM peptide tracer would be a promising lead compound for measuring TEM8 expression. Further efforts to improve the affinity and specificity of the tracer and to increase its metabolic stability are warranted. ..
  12. Tosh D, Chinn M, Ivanov A, Klutz A, Gao Z, Jacobson K. Functionalized congeners of A3 adenosine receptor-selective nucleosides containing a bicyclo[3.1.0]hexane ring system. J Med Chem. 2009;52:7580-92 pubmed publisher
    ..SAR parallels between the two series lost stringency at distal positions. The most potent and selective novel compounds were amine congener 15 (K(i) = 2.1 nM) and truncated partial agonist 22 (K(i) = 4.9 nM). ..
  13. Wickliffe K, Leppla S, Moayeri M. Killing of macrophages by anthrax lethal toxin: involvement of the N-end rule pathway. Cell Microbiol. 2008;10:1352-62 pubmed publisher
    ..We also show that LT-induced c-IAP1 degradation is independent of the IAP-antagonizing proteins Smac/DIABLO and Omi/HtrA2, but dependent on caspases. ..
  14. Yu A, Idle J, Herraiz T, Küpfer A, Gonzalez F. Screening for endogenous substrates reveals that CYP2D6 is a 5-methoxyindolethylamine O-demethylase. Pharmacogenetics. 2003;13:307-19 pubmed
    ..These processes may also impact on mental and neurological health. The findings may open new vistas for the determination of CYP2D6 phenotype. ..
  15. Nocek B, Tikhonov A, Babnigg G, Gu M, Zhou M, Makarova K, et al. Structural and functional characterization of microcin C resistance peptidase MccF from Bacillus anthracis. J Mol Biol. 2012;420:366-83 pubmed publisher
    ..We hypothesize that bacterial mccF genes serve as a source of bacterial antibiotic resistance. ..
  16. Singh S, Grimaud R, Hoskins J, Wickner S, Maurizi M. Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP. Proc Natl Acad Sci U S A. 2000;97:8898-903 pubmed
    ..ClpX preferentially targets motifs exposed in specific proteins. As the protein is unfolded by ClpX, additional motifs are exposed that facilitate its retention and favor its translocation to ClpP for degradation. ..
  17. Hoskins J, Wickner S. Two peptide sequences can function cooperatively to facilitate binding and unfolding by ClpA and degradation by ClpAP. Proc Natl Acad Sci U S A. 2006;103:909-14 pubmed
  18. Zhang J, Zhang K, Gao Z, Paoletta S, Zhang D, Han G, et al. Agonist-bound structure of the human P2Y12 receptor. Nature. 2014;509:119-22 pubmed publisher
  19. Louis J, Tözsér J, Roche J, Matúz K, Aniana A, Sayer J. Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 protease. Biochemistry. 2013;52:7678-88 pubmed publisher
    ..Linking of the subunits did not appreciably change the ΔTm on inhibitor binding; thus stabilization by tethering appears to have little direct effect on enhancing inhibitor affinity. ..
  20. Moskovitz J, Singh V, Requena J, Wilkinson B, Jayaswal R, Stadtman E. Purification and characterization of methionine sulfoxide reductases from mouse and Staphylococcus aureus and their substrate stereospecificity. Biochem Biophys Res Commun. 2002;290:62-5 pubmed publisher
    ..Also, we have shown that in Staphylococcus aureus there are two MsrA and one nonselenoprotein MsrB, which demonstrates the same substrate stereospecificity as the mouse MsrB...
  21. Lee C, Park M. Human deoxyhypusine synthase: interrelationship between binding of NAD and substrates. Biochem J. 2000;352 Pt 3:851-7 pubmed
  22. Fons R, Bogert B, Hegde R. Substrate-specific function of the translocon-associated protein complex during translocation across the ER membrane. J Cell Biol. 2003;160:529-39 pubmed
    ..These results identify the TRAP complex as a functional component of the translocon and demonstrate that it acts in a substrate-specific manner to facilitate the initiation of protein translocation. ..
  23. Auld D, Thorne N, Maguire W, Inglese J. Mechanism of PTC124 activity in cell-based luciferase assays of nonsense codon suppression. Proc Natl Acad Sci U S A. 2009;106:3585-90 pubmed publisher
    ..Our results demonstrate the value of understanding potential interactions between reporter enzymes and chemical compounds and emphasize the importance of implementing the appropriate control assays before interpreting HTS results. ..
  24. Chon H, Sparks J, Rychlik M, Nowotny M, Burgers P, Crouch R, et al. RNase H2 roles in genome integrity revealed by unlinking its activities. Nucleic Acids Res. 2013;41:3130-43 pubmed publisher
    ..However, this AGS-related mutation accumulates 2-5 bp deletions at a very similar rate as the deletion strain. ..
  25. Yamaguchi H, Durell S, Feng H, Bai Y, Anderson C, Appella E. Development of a substrate-based cyclic phosphopeptide inhibitor of protein phosphatase 2Cdelta, Wip1. Biochemistry. 2006;45:13193-202 pubmed
    ..These results provide the first proof of concept of a specific inhibitor of the catalytic site of Wip1 and should be useful for developing potential anti-cancer drugs. ..
  26. Parrish S, Moss B. Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses. J Virol. 2007;81:12973-8 pubmed
    ..Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner. ..
  27. Li W, Tu D, Li L, Wollert T, Ghirlando R, Brunger A, et al. Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2. Proc Natl Acad Sci U S A. 2009;106:3722-7 pubmed publisher
    ..Our data suggest that a large gp78-Ube2g2 heterooligomer brings multiple Ube2g2 molecules into close proximity, allowing ubiquitin moieties to be transferred between neighboring Ube2g2s to form active site-linked polyubiquitin chains. ..
  28. Ballestar E, Pile L, Wassarman D, Wolffe A, Wade P. A Drosophila MBD family member is a transcriptional corepressor associated with specific genes. Eur J Biochem. 2001;268:5397-406 pubmed
    ..This banding pattern suggests gene-specific regulatory functions for dMBD-like and the Drosophila Mi-2 complex. ..
  29. Suh P, Ryu S, Moon K, Suh H, Rhee S. Inositol phospholipid-specific phospholipase C: complete cDNA and protein sequences and sequence homology to tyrosine kinase-related oncogene products. Proc Natl Acad Sci U S A. 1988;85:5419-23 pubmed
    ..Therefore, this unexpected similarity raises the possibility that the 148-kDa phospholipase C and cytoplasmic tyrosine kinases are modulated by common cellular component(s). ..
  30. Pavlicek J, Sauzet S, Besseau L, Coon S, Weller J, Boeuf G, et al. Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus. BMC Evol Biol. 2010;10:154 pubmed publisher
  31. Fan Y, Wong L, Johnson G. EGFR kinase possesses a broad specificity for ErbB phosphorylation sites, and ligand increases catalytic-centre activity without affecting substrate binding affinity. Biochem J. 2005;392:417-23 pubmed
    ..The results also demonstrated that, unlike phosphorylation sites in select downstream targets, EGF does not regulate the recognition of phosphorylation sites in the C-terminal region of any of the ErbBs. ..
  32. Moskovitz J, Berlett B, Poston J, Stadtman E. The yeast peptide-methionine sulfoxide reductase functions as an antioxidant in vivo. Proc Natl Acad Sci U S A. 1997;94:9585-9 pubmed
    ..Also, the results support the proposition that MsrA possess an antioxidant function. The ability of MsrA to repair oxidative damage in vivo may be of singular importance if methionine residues serve as antioxidants. ..
  33. Armstrong M, Freedman C, Jung J, Zheng Y, Kalyanaraman C, Jacobson M, et al. A potent and selective inhibitor targeting human and murine 12/15-LOX. Bioorg Med Chem. 2016;24:1183-90 pubmed publisher
    ..0±3.3 μM. These data indicate that 99089 and related derivatives may serve as a starting point for the development of anti-stroke therapeutics due to their ability to selectively target h12/15-LOX in vitro and m12/15-LOX ex vivo. ..
  34. Ortega J, Lee H, Maurizi M, Steven A. ClpA and ClpX ATPases bind simultaneously to opposite ends of ClpP peptidase to form active hybrid complexes. J Struct Biol. 2004;146:217-26 pubmed
    ..Thus, ClpXAP is a bifunctional protease whose two ends can independently target different classes of substrates. ..
  35. Robey R, Honjo Y, Morisaki K, Nadjem T, Runge S, Risbood M, et al. Mutations at amino-acid 482 in the ABCG2 gene affect substrate and antagonist specificity. Br J Cancer. 2003;89:1971-8 pubmed
  36. Wang Z, Fan M, Candas D, Zhang T, Qin L, Eldridge A, et al. Cyclin B1/Cdk1 coordinates mitochondrial respiration for cell-cycle G2/M progression. Dev Cell. 2014;29:217-32 pubmed publisher
  37. Capitini C, Herby S, Milliron M, Anver M, Mackall C, Fry T. Bone marrow deficient in IFN-{gamma} signaling selectively reverses GVHD-associated immunosuppression and enhances a tumor-specific GVT effect. Blood. 2009;113:5002-9 pubmed publisher
  38. Parrish S, Resch W, Moss B. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc Natl Acad Sci U S A. 2007;104:2139-44 pubmed
    ..Although it may seem self-destructive for a virus to encode a decapping and a capping enzyme, accelerated mRNA turnover helps eliminate competing host mRNAs and allows stage-specific synthesis of viral proteins. ..
  39. Tang W, Li D, Li C, Esser L, Dai R, Guo L, et al. A novel ATP-dependent conformation in p97 N-D1 fragment revealed by crystal structures of disease-related mutants. EMBO J. 2010;29:2217-29 pubmed publisher
    ..We propose that IBMPFD mutations alter the timing of the transition between nucleotide states by destabilizing the ADP-bound form and consequently interfere with the interactions between the N-domains and their substrates. ..
  40. Koonin E, Tatusov R. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol. 1994;244:125-32 pubmed
    ..A specific role in the catalysis of the hydrolysis of carbon-halogen and other bonds is assigned to each of these residues. ..
  41. Olsen V, Cawley N, Brandt J, Egel Mitani M, Loh Y. Identification and characterization of Saccharomyces cerevisiae yapsin 3, a new member of the yapsin family of aspartic proteases encoded by the YPS3 gene. Biochem J. 1999;339 ( Pt 2):407-11 pubmed
    ..Cleavage of several prohormones by non-anchored yapsin 3 revealed a specificity distinct from that of yapsin 1. ..
  42. Ariyannur P, Moffett J, Manickam P, Pattabiraman N, Arun P, Nitta A, et al. Methamphetamine-induced neuronal protein NAT8L is the NAA biosynthetic enzyme: implications for specialized acetyl coenzyme A metabolism in the CNS. Brain Res. 2010;1335:1-13 pubmed publisher
    ..We conclude that NAA is a major storage and transport form of acetyl coenzyme A specific to the nervous system, thus linking it to both lipid synthesis and energy metabolism. ..
  43. Liao X, Buggey J, Kimmel A. Chemotactic activation of Dictyostelium AGC-family kinases AKT and PKBR1 requires separate but coordinated functions of PDK1 and TORC2. J Cell Sci. 2010;123:983-92 pubmed publisher
    ..Despite certain similarities, AKT and PKBR1 have distinct regulatory paths that impact activation and effector targeting, with PDK1 serving a central role. ..
  44. Samelson L, Egerton M, Thomas P, Wange R. The T cell antigen receptor tyrosine kinase pathway. Adv Exp Med Biol. 1992;323:9-16 pubmed
  45. Michishita E, Park J, Burneskis J, Barrett J, Horikawa I. Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol Biol Cell. 2005;16:4623-35 pubmed
  46. Heemskerk F, Chen H, Huang F. Protein kinase C phosphorylates Ser152, Ser156 and Ser163 but not Ser160 of MARCKS in rat brain. Biochem Biophys Res Commun. 1993;190:236-41 pubmed
    ..These results indicate that in vitro, PKC phosphorylates MARCKS only at three sites, but not at Ser160 as that reported previously, and there was no preferential phosphorylation of MARCKS by either PKC isozyme I, II or III. ..
  47. Gao R, Huang S, Marchand C, Pommier Y. Biochemical characterization of human tyrosyl-DNA phosphodiesterase 2 (TDP2/TTRAP): a Mg(2+)/Mn(2+)-dependent phosphodiesterase specific for the repair of topoisomerase cleavage complexes. J Biol Chem. 2012;287:30842-52 pubmed publisher
    ..Our study characterizes the substrate specificity and kinetic parameters of TDP2. In addition, a two-metal catalytic mechanism is proposed. ..
  48. Lazarus B, Love D, Hanover J. Recombinant O-GlcNAc transferase isoforms: identification of O-GlcNAcase, yes tyrosine kinase, and tau as isoform-specific substrates. Glycobiology. 2006;16:415-21 pubmed
    ..The identification of a tyrosine kinase and O-GlcNAcase as OGT targets suggests the potential for OGT participation in numerous signal transduction cascades. ..
  49. Lehnherr H, Yarmolinsky M. Addiction protein Phd of plasmid prophage P1 is a substrate of the ClpXP serine protease of Escherichia coli. Proc Natl Acad Sci U S A. 1995;92:3274-7 pubmed
    ..This conclusion situates P1 among plasmids that elicit severe withdrawal symptoms and are able to do so because they encode both a cell toxin and an actively degraded macromolecule that blocks the synthesis or function of the toxin...
  50. Jeong H, Backlund P, CHEN H, Karavanov A, Crouch R. RNase H2 of Saccharomyces cerevisiae is a complex of three proteins. Nucleic Acids Res. 2004;32:407-14 pubmed
    ..The multisubunit nature of S.cerevisiae RNase H2 may be important both for structural purposes and to provide a means of interacting with other proteins involved in DNA replication/repair and transcription. ..
  51. Xie Z, Zhang J, Siraganian R. Positive regulation of c-Jun N-terminal kinase and TNF-alpha production but not histamine release by SHP-1 in RBL-2H3 mast cells. J Immunol. 2000;164:1521-8 pubmed
    ..The substrate-trapping mutant SHP1/D419A identified pp25 and pp30 as two major potential substrates of SHP-1 in RBL-2H3 cells. Therefore, SHP-1 may play a role in allergy and inflammation by regulating mast cell cytokine production. ..
  52. Yusufzai T, Wolffe A. Functional consequences of Rett syndrome mutations on human MeCP2. Nucleic Acids Res. 2000;28:4172-9 pubmed
    ..Together, these results provide evidence of how Rett syndrome mutations can affect distinct functions of MeCP2 and give insight into these mutations that may contribute to the disease. ..
  53. Seo E, Liu F, Kawagishi Kobayashi M, Ung T, Cao C, Dar A, et al. Protein kinase PKR mutants resistant to the poxvirus pseudosubstrate K3L protein. Proc Natl Acad Sci U S A. 2008;105:16894-9 pubmed publisher
    ..We propose that these paradoxical effects of the PKR mutations on pseudosubstrate vs. substrate interactions reflect differences between the rigid K3L protein and the plastic nature of eIF2alpha around the Ser-51 phosphorylation site...
  54. Pouliot J, Robertson C, Nash H. Pathways for repair of topoisomerase I covalent complexes in Saccharomyces cerevisiae. Genes Cells. 2001;6:677-87 pubmed
    ..The efficiency of these pathways differs for complexes induced with the chemotherapeutic agent camptothecin vs. those accumulated by mutant forms of topoisomerase I. ..
  55. Lei H, Liu J, Fukushige T, Fire A, Krause M. Caudal-like PAL-1 directly activates the bodywall muscle module regulator hlh-1 in C. elegans to initiate the embryonic muscle gene regulatory network. Development. 2009;136:1241-9 pubmed publisher
    ..Together, these results provide a molecular framework for the gene regulatory network activating the muscle module during embryogenesis. ..
  56. Mukhopadhyay D, Ayaydin F, Kolli N, Tan S, Anan T, Kametaka A, et al. SUSP1 antagonizes formation of highly SUMO2/3-conjugated species. J Cell Biol. 2006;174:939-49 pubmed
    ..Together, our findings argue that SUSP1 may play a specialized role in dismantling highly conjugated SUMO2 and -3 species that is critical for PML body maintenance. ..
  57. Old S, Sato S, Kador P, Carper D. In vitro expression of rat lens aldose reductase in Escherichia coli. Proc Natl Acad Sci U S A. 1990;87:4942-5 pubmed
    ..This construction expresses an active enzyme that has been purified and demonstrates kinetic, immunological, and inhibitory properties similar to rat lens aldose reductase. ..
  58. Zheng Y, Li B, Rudrabhatla P, Shukla V, Amin N, Maric D, et al. Phosphorylation of p27Kip1 at Thr187 by cyclin-dependent kinase 5 modulates neural stem cell differentiation. Mol Biol Cell. 2010;21:3601-14 pubmed publisher
    ..Cdk5 phosphorylation of p27(Kip1), a modular molecule, may regulate the progress of neuronal differentiation from cell cycle arrest through differentiation, neurite outgrowth, and migration. ..
  59. Zhang Y, Chang C, Gehling D, Hemmati Brivanlou A, Derynck R. Regulation of Smad degradation and activity by Smurf2, an E3 ubiquitin ligase. Proc Natl Acad Sci U S A. 2001;98:974-9 pubmed
  60. Kimura A, Kim H. Phosphatidylserine synthase 2: high efficiency for synthesizing phosphatidylserine containing docosahexaenoic acid. J Lipid Res. 2013;54:214-22 pubmed publisher
    ..These findings suggest that PSS2 may play a key role in PS accumulation in brain and testis through high activity toward DHA-containing substrates that are abundant in these tissues. ..
  61. Wan F, Anderson D, Barnitz R, Snow A, Bidere N, Zheng L, et al. Ribosomal protein S3: a KH domain subunit in NF-kappaB complexes that mediates selective gene regulation. Cell. 2007;131:927-39 pubmed
    ..Our observations provide insight into how NF-kappaB selectively controls gene expression. ..
  62. Nowotny M, Cerritelli S, Ghirlando R, Gaidamakov S, Crouch R, Yang W. Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD. EMBO J. 2008;27:1172-81 pubmed publisher
    ..Similar activity enhancement by small substrate-binding domains linked to the catalytic domain likely occurs in other nucleic acid enzymes. ..
  63. Trievel R, Beach B, Dirk L, Houtz R, Hurley J. Structure and catalytic mechanism of a SET domain protein methyltransferase. Cell. 2002;111:91-103 pubmed
    ..The cofactor enters by a "back door" on the opposite side of the enzyme from substrate, promoting highly specific protein recognition and allowing addition of multiple methyl groups. ..
  64. Wolff E, Kang K, Kim Y, Park M. Posttranslational synthesis of hypusine: evolutionary progression and specificity of the hypusine modification. Amino Acids. 2007;33:341-50 pubmed
  65. Hong S, Cho Y, Yu L, Yu H, Veenstra T, Ge K. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc Natl Acad Sci U S A. 2007;104:18439-44 pubmed
  66. Tamura T, Stadtman T. A new selenoprotein from human lung adenocarcinoma cells: purification, properties, and thioredoxin reductase activity. Proc Natl Acad Sci U S A. 1996;93:1006-11 pubmed
    ..The selenocysteine-containing TR from the adenocarcinoma cells may be a variant form distinct from rat liver TR. ..
  67. Handa V, Saha T, Usdin K. The fragile X syndrome repeats form RNA hairpins that do not activate the interferon-inducible protein kinase, PKR, but are cut by Dicer. Nucleic Acids Res. 2003;31:6243-8 pubmed
    ..In addition, RNA hairpins may also account for the stalling of the 40S ribosomal subunit that is thought to contribute to the translation deficit in fragile X pre-mutation and full mutation alleles. ..
  68. Hoskins J, Yanagihara K, Mizuuchi K, Wickner S. ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence. Proc Natl Acad Sci U S A. 2002;99:11037-42 pubmed
    ..We also found that ClpA recognizes the NH2-terminal 15 aa RepA tag, when it is fused to the COOH terminus of GFP. Moreover, ClpA recognizes the RepA tag in either the authentic or inverse orientation. ..
  69. Ishibashi T, Bottaro D, Chan A, Miki T, Aaronson S. Expression cloning of a human dual-specificity phosphatase. Proc Natl Acad Sci U S A. 1992;89:12170-4 pubmed
    ..These properties suggest that VHR is capable of regulating intracellular events mediated by both tyrosine and serine phosphorylation. ..
  70. Han G, Gupta S, Gable K, Niranjanakumari S, Moitra P, Eichler F, et al. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. Proc Natl Acad Sci U S A. 2009;106:8186-91 pubmed publisher
  71. Jones J, Gellert M. Ordered assembly of the V(D)J synaptic complex ensures accurate recombination. EMBO J. 2002;21:4162-71 pubmed
    ..Additional cellular factors such as chromatin may ensure that RAG1/2 first assembles on a 12 RSS, and then a free 23 RSS enters to activate cleavage. ..
  72. Stan G, Brooks B, Lorimer G, Thirumalai D. Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state. Proc Natl Acad Sci U S A. 2006;103:4433-8 pubmed
    ..The diversity of secondary structures implies that there are large and varied conformational transitions in the recognition motifs after their displacement by the mobile loops of GroES. ..
  73. Nagata K, Martin B, Gillette J, Sasame H. Isozymes of cytochrome P-450 that metabolize naphthalene in liver and lung of untreated mice. Drug Metab Dispos. 1990;18:557-64 pubmed
    ..Thus, P-450m50b probably is not orthologous to cytochrome P-450c.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  74. Niimi T, Munakata M, Keck Waggoner C, Popescu N, Levitt R, Hisada M, et al. A polymorphism in the human UGRP1 gene promoter that regulates transcription is associated with an increased risk of asthma. Am J Hum Genet. 2002;70:718-25 pubmed
    ..1 times more likely to have asthma than were those with the wild-type allele (G/G). ..
  75. Um J, Brown A, Singh S, Chen Y, Gucek M, Lee B, et al. Metabolic sensor AMPK directly phosphorylates RAG1 protein and regulates V(D)J recombination. Proc Natl Acad Sci U S A. 2013;110:9873-8 pubmed publisher
    ..Our results suggest that V(D)J recombination can be regulated by AMPK activation, providing a potential new link between metabolic stress and development of B and T lymphocytes. ..
  76. Thorne N, Shen M, Lea W, Simeonov A, Lovell S, Auld D, et al. Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter. Chem Biol. 2012;19:1060-72 pubmed publisher
    ..As in some cell-based FLuc reporter assays, compounds acting as FLuc inhibitors yield paradoxical luminescence increases, thus data on compounds acquired from FLuc-dependent assays require careful analysis as described here. ..
  77. Vahedi S, Chufan E, Ambudkar S. Global alteration of the drug-binding pocket of human P-glycoprotein (ABCB1) by substitution of fifteen conserved residues reveals a negative correlation between substrate size and transport efficiency. Biochem Pharmacol. 2017;143:53-64 pubmed publisher
    ..This was further supported by the physico-chemical characterization of seventeen tested substrates, which revealed a negative correlation between drug transport and molecular size for the tyrosine-enriched P-gp mutant. ..
  78. Chae J, Wood G, Richard K, Jaffe H, Colburn N, Masters S, et al. The familial Mediterranean fever protein, pyrin, is cleaved by caspase-1 and activates NF-kappaB through its N-terminal fragment. Blood. 2008;112:1794-803 pubmed publisher
    ..Our data support a new pyrin/caspase-1 pathway for NF-kappaB activation. ..
  79. Gomez Quiroz L, Factor V, Kaposi Novak P, Coulouarn C, Conner E, Thorgeirsson S. Hepatocyte-specific c-Met deletion disrupts redox homeostasis and sensitizes to Fas-mediated apoptosis. J Biol Chem. 2008;283:14581-9 pubmed publisher
    ..These data provide evidence that intact c-Met signaling is a critical factor in the protection against excessive generation of endogenous reactive oxygen species. ..
  80. De Silva F, Paran N, Moss B. Products and substrate/template usage of vaccinia virus DNA primase. Virology. 2009;383:136-41 pubmed publisher
    ..The absence of stringent template specificity is consistent with a role for the enzyme in priming DNA synthesis at the replication fork. ..
  81. Kimchi Sarfaty C, Oh J, Kim I, Sauna Z, Calcagno A, Ambudkar S, et al. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science. 2007;315:525-8 pubmed
  82. Morley S, Sung J, Sun G, Martelli M, Bunnell S, Bierer B. Gelsolin overexpression alters actin dynamics and tyrosine phosphorylation of lipid raft-associated proteins in Jurkat T cells. Mol Immunol. 2007;44:2469-80 pubmed
    ..Thus, our data indicate that actin cytoskeletal dynamics modulate the tyrosine phosphorylation of raft-associated proteins and subsequent downstream signal transduction. ..
  83. Szabo R, Netzel Arnett S, Hobson J, Antalis T, Bugge T. Matriptase-3 is a novel phylogenetically preserved membrane-anchored serine protease with broad serpin reactivity. Biochem J. 2005;390:231-42 pubmed
    ..Our study identifies matriptase-3 as a novel biologically active TTSP of the matriptase subfamily having a unique expression pattern and post-translational regulation. ..
  84. Thompson J, Hess S, Pikis A. Genes malh and pagl of Clostridium acetobutylicum ATCC 824 encode NAD+- and Mn2+-dependent phospho-alpha-glucosidase(s). J Biol Chem. 2004;279:1553-61 pubmed publisher
    ..Of the two putative operons, our findings suggest that only proteins encoded by the mal operon participate in the dissimilation of maltose and related O-alpha-linked glucosides by C. acetobutylicum 824...
  85. Compton E, Taylor E, Mindell J. The 3-4 loop of an archaeal glutamate transporter homolog experiences ligand-induced structural changes and is essential for transport. Proc Natl Acad Sci U S A. 2010;107:12840-5 pubmed publisher
    ..These results inculcate the 3-4 loop as an important player in the transport process, a finding not predicted by any of the available crystal structures of Glt(Ph). ..
  86. Cerritelli S, Crouch R. Ribonuclease H: the enzymes in eukaryotes. FEBS J. 2009;276:1494-505 pubmed publisher
    ..Mutations in any of the three subunits of human RNase H2 cause Aicardi-Goutières syndrome, a human neurological disorder with devastating consequences. ..
  87. Braddock D, Baber J, Levens D, Clore G. Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA. EMBO J. 2002;21:3476-85 pubmed
  88. Gonzalez M, Frank E, Levine A, Woodgate R. Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis. Genes Dev. 1998;12:3889-99 pubmed
  89. Thompson J, Gentry Weeks C, Nguyen N, Folk J, Robrish S. Purification from Fusobacterium mortiferum ATCC 25557 of a 6-phosphoryl-O-alpha-D-glucopyranosyl:6-phosphoglucohydrolase that hydrolyzes maltose 6-phosphate and related phospho-alpha-D-glucosides. J Bacteriol. 1995;177:2505-12 pubmed
    ..mortiferum. Synthesis of 6-phospho-alpha-glucosidase increased dramatically during growth of the organism on alpha-glucosides, such as maltose, alpha-methylglucoside, trehalose, turanose, and palatinose...