Experts and Doctors on conserved sequence in Bethesda, Maryland, United States


Locale: Bethesda, Maryland, United States
Topic: conserved sequence

Top Publications

  1. Balaji S, Iyer L, Aravind L. HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes. Mol Biosyst. 2009;5:269-75 pubmed publisher
    ..Hence, we propose that Hpc2p homologs are probably involved in recruitment of the ancient conserved histone-loading Hir-Asf1 complex to different lineage-specific chromatin reorganization processes. ..
  2. Hudson R, Yi M, Volfovsky N, Prueitt R, Esposito D, Volinia S, et al. Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer. Mol Cancer. 2013;12:13 pubmed publisher
    ..This first study of ucRNA expression in human prostate cancer indicates an altered transcript expression in the disease. ..
  3. Hwang C, D Souza U, Eisch A, Yajima S, Lammers C, Yang Y, et al. Dopamine receptor regulating factor, DRRF: a zinc finger transcription factor. Proc Natl Acad Sci U S A. 2001;98:7558-63 pubmed
    ..The latter observations provide a basis for dopamine receptor regulation after these manipulations. We conclude that DRRF is important for modulating dopaminergic transmission in the brain. ..
  4. Anikster Y, Kleta R, Shaag A, Gahl W, Elpeleg O. Type III 3-methylglutaconic aciduria (optic atrophy plus syndrome, or Costeff optic atrophy syndrome): identification of the OPA3 gene and its founder mutation in Iraqi Jews. Am J Hum Genet. 2001;69:1218-24 pubmed
    ..Milder mutations in OPA3 should be sought in patients with optic atrophy with later onset, even in the absence of additional neurological abnormalities. ..
  5. Iyer L, Koonin E, Aravind L. Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. Genome Biol. 2002;3:RESEARCH0012 pubmed
    ..We also demonstrate the extensive role of lineage-specific gene expansion and domain shuffling, within a limited set of approximately 24 domains, in the generation of the diversity of virus-specific regulatory proteins. ..
  6. Lipman D, Souvorov A, Koonin E, Panchenko A, Tatusova T. The relationship of protein conservation and sequence length. BMC Evol Biol. 2002;2:20 pubmed
    ..For all the organisms studied, there seems to be a significant evolutionary trend favoring shorter proteins in the absence of other, more specific functional constraints. ..
  7. Zhao M, Gold L, Dorward H, Liang L, Hoodbhoy T, Boja E, et al. Mutation of a conserved hydrophobic patch prevents incorporation of ZP3 into the zona pellucida surrounding mouse eggs. Mol Cell Biol. 2003;23:8982-91 pubmed
    ..The cleavage site that releases the ectodomain from the transmembrane domain was defined by mass spectrometry of native zonae pellucidae and lies N-terminal to a proprotein convertase site that is distinct from the hydrophobic patch. ..
  8. Crotti L, Basrai M. Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J. 2004;23:1804-14 pubmed
    ..Our results highlight the evolutionary conservation of pathways required for genome stability in yeast and humans. ..
  9. Xia D, Esser L, Yu L, Yu C. Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc1 complex. Photosynth Res. 2007;92:17-34 pubmed

More Information

Publications133 found, 100 shown here

  1. Wolf J, Palmby T, Gavard J, Williams B, Gutkind J. Multiple PPPS/TP motifs act in a combinatorial fashion to transduce Wnt signaling through LRP6. FEBS Lett. 2008;582:255-61 pubmed
    ..Instead, we show that each LRP6 PPPS/TP motif contributes in a combinatorial fashion to activate the canonical Wnt-beta-catenin pathway. ..
  2. Liu H, Rahman A, Semino Mora C, Doi S, Dubois A. Specific and sensitive detection of H. pylori in biological specimens by real-time RT-PCR and in situ hybridization. PLoS ONE. 2008;3:e2689 pubmed publisher
    ..This H. pylori-specific region of the 16S rRNA sequence is highly conserved among most H. pylori strains and allows specific detection, identification, and quantification of this bacterium in biological specimens. ..
  3. Bennett C, Green J. Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models. Breast Cancer Res. 2008;10:213 pubmed publisher
  4. Yutin N, Wolf M, Wolf Y, Koonin E. The origins of phagocytosis and eukaryogenesis. Biol Direct. 2009;4:9 pubmed publisher
    ..The acquisition of the endosymbiont triggered eukaryogenesis, in particular, the emergence of the endomembrane system that eventually led to the evolution of modern-type phagocytosis, independently in several eukaryotic lineages. ..
  5. Yang W. Topoisomerases and site-specific recombinases: similarities in structure and mechanism. Crit Rev Biochem Mol Biol. 2010;45:520-34 pubmed publisher
    ..This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation. ..
  6. Hansman G, Biertümpfel C, Georgiev I, McLellan J, Chen L, Zhou T, et al. Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. J Virol. 2011;85:6687-701 pubmed publisher
    ..Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus. ..
  7. Rogozin I, Carmel L, Csuros M, Koonin E. Origin and evolution of spliceosomal introns. Biol Direct. 2012;7:11 pubmed publisher
  8. Kato H, Jiang J, Zhou B, Rozendaal M, Feng H, Ghirlando R, et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science. 2013;340:1110-3 pubmed publisher
    ..Our findings reveal a conserved mechanism for protein recruitment to centromeres and a histone recognition mode whereby a disordered peptide binds the histone tail through hydrophobic interactions facilitated by nucleosome docking...
  9. Gong D, Hashimoto S, Wada K, Roeder R, Nakatani Y, Horikoshi M. Imperfect conservation of a sigma factor-like subregion in Xenopus general transcription factor RAP30. Nucleic Acids Res. 1992;20:6414 pubmed
  10. Buczko E, Koh Y, Miyagawa Y, Dufau M. The rat 17 alpha-hydroxylase-17,20-desmolase (CYP17) active site: computerized homology modeling and site directed mutagenesis. J Steroid Biochem Mol Biol. 1995;52:209-18 pubmed
    ..These studies demonstrate that exon 6 of the rat CYP17 is essential for CYP17 activity, and may be structurally related to the NAD-linked prokaryote alpha/beta F supersecondary element. ..
  11. Tatusov R, Altschul S, Koonin E. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci U S A. 1994;91:12091-5 pubmed
    ..The procedure described was used to detect novel conserved motifs of potential biological importance. ..
  12. Clark J, Moore L, Krasinskas A, Way J, Battey J, Tamkun J, et al. Selective amplification of additional members of the ADP-ribosylation factor (ARF) family: cloning of additional human and Drosophila ARF-like genes. Proc Natl Acad Sci U S A. 1993;90:8952-6 pubmed
    ..The latter proteins currently comprise two distinct gene products in Drosophila (arl and ARL84F) and one in man (ARL2). ..
  13. Mazumder R, Iyer L, Vasudevan S, Aravind L. Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nucleic Acids Res. 2002;30:5229-43 pubmed
    ..Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution. ..
  14. Tsang M, Maegawa S, Kiang A, Habas R, Weinberg E, Dawid I. A role for MKP3 in axial patterning of the zebrafish embryo. Development. 2004;131:2769-79 pubmed
    ..Thus, mkp3 encodes a feedback attenuator of the FGF pathway, the expression of which is initiated at an early stage so as to ensure correct FGF signaling levels at the time of axial patterning. ..
  15. Seydel K, Gaur D, Aravind L, Subramanian G, Miller L. Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains. Exp Parasitol. 2005;110:389-93 pubmed
    ..falciparum. The timing of expression as well as the location of this protein suggests that it may play an important role in the sorting of proteins to the apical organelles during the development of the asexual stage of the parasite. ..
  16. Angerer L, Hussain S, Wei Z, Livingston B. Sea urchin metalloproteases: a genomic survey of the BMP-1/tolloid-like, MMP and ADAM families. Dev Biol. 2006;300:267-81 pubmed
    ..The genome sequence now opens the door to experimental manipulations designed to understand how modulation of the extracellular environment affects development. ..
  17. Przytycka T, Jothi R, Aravind L, Lipman D. Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evol Biol. 2008;8:208 pubmed publisher
    ..In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer. ..
  18. Pos Z, Selleri S, Spivey T, Wang J, Liu H, Worschech A, et al. Genomic scale analysis of racial impact on response to IFN-alpha. Proc Natl Acad Sci U S A. 2010;107:803-8 pubmed publisher
  19. Marchler Bauer A, Lu S, Anderson J, Chitsaz F, Derbyshire M, DeWeese Scott C, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011;39:D225-9 pubmed publisher
    ..CDD can be accessed via ..
  20. Moss B. Poxvirus cell entry: how many proteins does it take?. Viruses. 2012;4:688-707 pubmed publisher
    ..Biochemical studies support a two-step process in which lipid mixing of viral and cellular membranes is followed by pore expansion and core penetration. ..
  21. Koonin E, Csuros M, Rogozin I. Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes. Wiley Interdiscip Rev RNA. 2013;4:93-105 pubmed publisher
    ..Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins. ..
  22. Marchler Bauer A, Zheng C, Chitsaz F, Derbyshire M, Geer L, Geer R, et al. CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2013;41:D348-52 pubmed publisher
    ..To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts. ..
  23. Rohan P, Davis P, Moskaluk C, Kearns M, Krutzsch H, Siebenlist U, et al. PAC-1: a mitogen-induced nuclear protein tyrosine phosphatase. Science. 1993;259:1763-6 pubmed
    ..PAC-1 was predominantly expressed in hematopoietic tissues and localized to the nucleus in transfected COS-7 cells and in mitogen-stimulated T cells. ..
  24. Komatsu K, Driscoll W, Koh Y, Strott C. A P-loop related motif (GxxGxxK) highly conserved in sulfotransferases is required for binding the activated sulfate donor. Biochem Biophys Res Commun. 1994;204:1178-85 pubmed
    ..These data strongly support the notion that the P-loop motif found in all cloned sulfotransferases constitutes, at least in part, the PAPS binding site for these enzymes. ..
  25. Chedid M, Michieli P, Lengel C, Huppi K, Givol D. A single nucleotide substitution at codon 31 (Ser/Arg) defines a polymorphism in a highly conserved region of the p53-inducible gene WAF1/CIP1. Oncogene. 1994;9:3021-4 pubmed
  26. Abe T, Kikuchi T, Chang T, Shinohara T. The sequence of the mouse phosducin-encoding gene and its 5'-flanking region. Gene. 1993;133:179-86 pubmed
    ..In addition, we found more than one similar Pd gene and two different mRNAs. The P1-AT clone encodes one of the Pd mRNAs. These results open the possibility that the multiple Pd genes encode multiple Pd. ..
  27. Iacangelo A, Eiden L. Chromogranin A: current status as a precursor for bioactive peptides and a granulogenic/sorting factor in the regulated secretory pathway. Regul Pept. 1995;58:65-88 pubmed
  28. Zhang J, Luo G, Herrera A, Paterson B, Horowits R. cDNA cloning of mouse nebulin. Evidence that the nebulin-coding sequence is highly conserved among vertebrates. Eur J Biochem. 1996;239:835-41 pubmed
    ..The sequence and Southern-blot data suggest that the nebulin sequence is highly conserved among vertebrate species. ..
  29. van Rhee A, Fischer B, van Galen P, Jacobson K. Modelling the P2Y purinoceptor using rhodopsin as template. Drug Des Discov. 1995;13:133-54 pubmed
  30. Hamasaki Katagiri N, Tabor C, Tabor H. Spermidine biosynthesis in Saccharomyces cerevisae: polyamine requirement of a null mutant of the SPE3 gene (spermidine synthase). Gene. 1997;187:35-43 pubmed
    ..This requirement is satisfied by a very low concentration of spermidine (10(-8) M) or a higher concentration of spermine (10(-6) M). ..
  31. Aravind L, Dixit V, Koonin E. Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. Science. 2001;291:1279-84 pubmed
    ..A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis. ..
  32. Phornphutkul C, Anikster Y, Huizing M, Braun P, Brodie C, Chou J, et al. The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, CARKL, and causes cystinosis if mutated in a critical region. Am J Hum Genet. 2001;69:712-21 pubmed
    ..These findings suggest that the CTNS promoter region should be examined in patients with cystinosis who have fewer than two coding-sequence mutations. ..
  33. Leipe D, Wolf Y, Koonin E, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002;317:41-72 pubmed
    ..In addition to the classification of previously known families of GTPases and related ATPases, we introduce several previously undetected families and describe new functional predictions. ..
  34. Renou J, Bierie B, Miyoshi K, Cui Y, Djiane J, Reichenstein M, et al. Identification of genes differentially expressed in mouse mammary epithelium transformed by an activated beta-catenin. Oncogene. 2003;22:4594-610 pubmed
    ..Lastly, stabilization of beta-catenin resulted in the retention of differentiated epithelium upon involution and altered activities of several proteases in transdifferentiated mammary epithelium. ..
  35. Gavard J, Gutkind J. VEGF controls endothelial-cell permeability by promoting the beta-arrestin-dependent endocytosis of VE-cadherin. Nat Cell Biol. 2006;8:1223-34 pubmed publisher
  36. Noguchi K, Vassilev A, Ghosh S, Yates J, DePamphilis M. The BAH domain facilitates the ability of human Orc1 protein to activate replication origins in vivo. EMBO J. 2006;25:5372-82 pubmed
    ..Thus, the BAH domain in human Orc1 facilitates its ability to activate replication origins in vivo by promoting association of ORC with chromatin. ..
  37. Puigbò P, Wolf Y, Koonin E. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol. 2009;8:59 pubmed publisher
  38. Yutin N, Koonin E. Archaeal origin of tubulin. Biol Direct. 2012;7:10 pubmed publisher
    ..These findings expand the emerging picture of the origin of key components of eukaryotic functional systems from ancestral forms that are scattered among the extant archaea. ..
  39. Joo J, Song J, Baik S, Lee W, Cho M, Lee K, et al. Genetic organization and conjugal plasmid DNA transfer of pHP69, a plasmid from a Korean isolate of Helicobacter pylori. J Microbiol. 2012;50:955-61 pubmed publisher
    ..It was shown that this vector could stably replicate and be mobilized among clinical H. pylori strains and demonstrated to gene transfer by natural plasmid. ..
  40. Zhang P, Maruyama T, Konkel J, Abbatiello B, Zamarron B, Wang Z, et al. PARP-1 controls immunosuppressive function of regulatory T cells by destabilizing Foxp3. PLoS ONE. 2013;8:e71590 pubmed publisher
    ..Thus, our data reveal a role for PARP-1 in controlling the function of Tregs through modulation of the stable expression of Foxp3. ..
  41. Tang W, Xia D. Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain. Sci Rep. 2016;6:20037 pubmed publisher
  42. Erlandson K, Bisht H, Weisberg A, Hyun S, Hansen B, Fischer E, et al. Poxviruses Encode a Reticulon-Like Protein that Promotes Membrane Curvature. Cell Rep. 2016;14:2084-2091 pubmed publisher
    ..We suggest that A17 is a viral reticulon-like protein that contributes to curvature during biogenesis of the poxvirus membrane. ..
  43. Jungwirth C, Rebbert M, Ozato K, Degen H, Schultz U, Dawid I. Chicken interferon consensus sequence-binding protein (ICSBP) and interferon regulatory factor (IRF) 1 genes reveal evolutionary conservation in the IRF gene family. Proc Natl Acad Sci U S A. 1995;92:3105-9 pubmed
  44. Brady J, Piatigorsky J. A mouse cDNA encoding a protein with zinc-fingers and a KRAB domain shows similarity to human profilaggrin. Gene. 1994;149:299-304 pubmed
    ..Sequences that hybridize to this cDNA are detectable in ten other mammalian species. ..
  45. Jensen J, Cenciarelli C, Hou D, Rellahan B, Dean M, Weissman A. T cell antigen receptor-eta subunit. Low levels of expression and limited cross-species conservation. J Immunol. 1993;150:122-30 pubmed
  46. Haynes S. Primary structure of Drosophila ribosomal protein L14 and identification of conserved protein motifs. DNA Seq. 1997;8:105-8 pubmed
    ..The sizes of the L14 proteins vary between different species, with most of the variability confined to the C-terminal region. ..
  47. Becker K, Lee I, Nagle J, Canning R, Gado A, Torres R, et al. C2H2-171: a novel human cDNA representing a developmentally regulated POZ domain/zinc finger protein preferentially expressed in brain. Int J Dev Neurosci. 1997;15:891-9 pubmed
    ..These data suggest that C2H2-171 may play an important role in vertebrate brain development and function. ..
  48. Stoughton D, Zapata G, Picone R, Vann W. Identification of Arg-12 in the active site of Escherichia coli K1 CMP-sialic acid synthetase. Biochem J. 1999;343 Pt 2:397-402 pubmed
    ..Steady-state kinetic analysis reveals changes in k(cat), K(m) and K(s) for CTP, which implicates Arg-12 in catalysis and substrate binding. ..
  49. Teng M, Collins P. The central conserved cystine noose of the attachment G protein of human respiratory syncytial virus is not required for efficient viral infection in vitro or in vivo. J Virol. 2002;76:6164-71 pubmed
    ..Thus, although the G protein is necessary for efficient virus replication in vivo, this activity does not require the central conserved cystine noose region. ..
  50. Anantharaman V, Aravind L. The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism. Genome Biol. 2002;3:RESEARCH0061 pubmed
    ..Identification of this versatile domain in numerous proteins could aid investigation of unexplored aspects of their biology. ..
  51. Lee J, Pestova T, Shin B, Cao C, Choi S, Dever T. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc Natl Acad Sci U S A. 2002;99:16689-94 pubmed
    ..Thus, in contrast to bacteria where the single GTPase IF2 is sufficient to catalyze translation initiation, eukaryotic cells require hydrolysis of GTP by both eIF2 and eIF5B to complete translation initiation. ..
  52. Nielsen K, VALASEK L, Sykes C, Jivotovskaya A, Hinnebusch A. Interaction of the RNP1 motif in PRT1 with HCR1 promotes 40S binding of eukaryotic initiation factor 3 in yeast. Mol Cell Biol. 2006;26:2984-98 pubmed
    ..Thus, the PRT1 RNP1 motif coordinates the functions of HCR1 and TIF32 in 40S binding of eIF3 and is needed for optimal preinitiation complex assembly and AUG recognition in vivo. ..
  53. Dewey C, Rogozin I, Koonin E. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics. 2006;7:311 pubmed
    ..Taken together, these findings attest to a compensatory relationship between splice sites and exonic splicing signals, depending on intron length. ..
  54. Horvath A, Giatzakis C, Tsang K, GREENE E, Osorio P, Boikos S, et al. A cAMP-specific phosphodiesterase (PDE8B) that is mutated in adrenal hyperplasia is expressed widely in human and mouse tissues: a novel PDE8B isoform in human adrenal cortex. Eur J Hum Genet. 2008;16:1245-53 pubmed publisher
    ..We conclude that PDE8B is another PDE gene linked to iMAD; it is a candidate causative gene for other adrenocortical lesions linked to the cAMP signaling pathway and possibly for tumors in other tissues. ..
  55. Rayavara K, Rajapandi T, Wollenberg K, Kabat J, Fischer E, Desai S. A complex of three related membrane proteins is conserved on malarial merozoites. Mol Biochem Parasitol. 2009;167:135-43 pubmed publisher
    ..Because all three genes are highly conserved in apicomplexan parasites, the complex formed by their encoded proteins likely serves an essential role for invasive merozoites. ..
  56. Roy S. Intronization, de-intronization and intron sliding are rare in Cryptococcus. BMC Evol Biol. 2009;9:192 pubmed publisher
    ..These results suggest that intronization, de-intronization, and intron boundary movement are rare events in evolution. ..
  57. Durand S, Storz G. Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol. 2010;75:1215-31 pubmed publisher
    ..We thus suggest that FnrS extends the FNR regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions. ..
  58. Tao R, Coleman M, Pennington J, Ozden O, Park S, Jiang H, et al. Sirt3-mediated deacetylation of evolutionarily conserved lysine 122 regulates MnSOD activity in response to stress. Mol Cell. 2010;40:893-904 pubmed publisher
    ..Finally, IR was unable to induce MnSOD deacetylation or activity in Sirt3?/? livers, and these irradiated livers displayed significant IR-induced cell damage and microvacuolization in their hepatocytes. ..
  59. Malicet C, Rochman M, Postnikov Y, Bustin M. Distinct properties of human HMGN5 reveal a rapidly evolving but functionally conserved nucleosome binding protein. Mol Cell Biol. 2011;31:2742-55 pubmed publisher
    ..HMGN5 has a highly disordered structure, binds dynamically to nucleosome core particles, modulates the binding of H1 to chromatin, reduces the compaction of the chromatin fiber, and affects transcription. ..
  60. Maldonado Baez L, Cole N, KRAMER H, Donaldson J. Microtubule-dependent endosomal sorting of clathrin-independent cargo by Hook1. J Cell Biol. 2013;201:233-47 pubmed publisher
    ..Loss of Hook1 also led to an inhibition of cell spreading, implicating a role for Hook1 sorting of specific CIE cargo proteins away from bulk membrane and back to the PM. ..
  61. Fong J, Murphy T, Pruitt K. Comparison of RefSeq protein-coding regions in human and vertebrate genomes. BMC Genomics. 2013;14:654 pubmed publisher
  62. Eren E, Zamuda K, Patton J. Modeling of the rotavirus group C capsid predicts a surface topology distinct from other rotavirus species. Virology. 2016;487:150-62 pubmed publisher
    ..In addition, our results showed a smaller RVC VP4 foot, which protrudes toward the intermediate VP6 layer, in comparison to that of RVA. Finally, our results showed major structural differences at the VP8* glycan recognition sites. ..
  63. 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. ..
  64. Makarova K, Mironov A, Gelfand M. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2001;2:RESEARCH0013 pubmed
    ..All genomes studied except M. tuberculosis contain ABC transport cassettes (related to the Art system of E. coli) belonging to the candidate arginine regulons. ..
  65. Rossi M, Demidov O, Anderson C, Appella E, Mazur S. Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites. Nucleic Acids Res. 2008;36:7168-80 pubmed publisher
    ..In cells containing wild-type p53, exposure to UV resulted in increased PPM1D protein levels even when PPM1D mRNA levels remained constant, indicating post-transcriptional regulation of PPM1D protein levels. ..
  66. Kuzin A, Kundu M, Ekatomatis A, Brody T, Odenwald W. Conserved sequence block clustering and flanking inter-cluster flexibility delineate enhancers that regulate nerfin-1 expression during Drosophila CNS development. Gene Expr Patterns. 2009;9:65-72 pubmed publisher
    ..In summary, EvoPrinter facilitates the discovery and analysis of enhancers that control crucial aspects of nerfin-1 expression. ..
  67. Neuwald A, Green P. Detecting patterns in protein sequences. J Mol Biol. 1994;239:698-712 pubmed
    ..In a search of a large set of sequences for internal repeats, the method detected novel ankyrin-like repeats in an Escherichia coli protein. ..
  68. Cao X, Kozak C, Liu Y, Noguchi M, O Connell E, Leonard W. Characterization of cDNAs encoding the murine interleukin 2 receptor (IL-2R) gamma chain: chromosomal mapping and tissue specificity of IL-2R gamma chain expression. Proc Natl Acad Sci U S A. 1993;90:8464-8 pubmed
    ..The cloning of the murine IL-2R gamma cDNA will facilitate the investigation of the role of this protein in lymphocyte function and thymic development. ..
  69. Koonin E. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 1996;24:2411-5 pubmed
    ..These particular RNA modifications and the respective enzymes are likely to be essential for the functioning of any cell. ..
  70. McGowan M, Neubauer J, Stolle C. Characterization of the rat carbonic anhydrase II gene structure: sequence analysis of the 5' flanking region and 3' UTR. Gene. 1997;186:181-8 pubmed
    ..Northern blot analysis reveals that the 1.7 kb rat CA II mRNA is abundantly expressed in adult male brain and kidney, while negligible amounts are detected in heart and liver. ..
  71. Zeng H, Kaul S, Simons S. Genomic organization of human GMEB-1 and rat GMEB-2: structural conservation of two multifunctional proteins. Nucleic Acids Res. 2000;28:1819-29 pubmed
    ..These results indicate that the GMEBs are proteins that evolved from a single parent gene, have been highly conserved since the divergence of rats and humans and probably play important roles in development and differentiation. ..
  72. Zhang H, Meng L, Zimonjic D, Popescu N, Pommier Y. Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases. Nucleic Acids Res. 2004;32:2087-92 pubmed
    ..We hypothesize that the prototype topoisomerase IB with the 13-exon structure formed first, and then duplicated. One topoisomerase specialized for nuclear DNA and the other for mitochondrial DNA. ..
  73. Goh S, Lee Y, Bhanu N, Cam M, Desper R, Martin B, et al. A newly discovered human alpha-globin gene. Blood. 2005;106:1466-72 pubmed
    ..These results suggest the human genome encodes a previously unrecognized globin member of the avian alpha-D family that is transcribed in a highly regulated pattern in erythroid cells. ..
  74. Poliakov E, Gentleman S, Cunningham F, Miller Ihli N, Redmond T. Key role of conserved histidines in recombinant mouse beta-carotene 15,15'-monooxygenase-1 activity. J Biol Chem. 2005;280:29217-23 pubmed
    ..These data are discussed in the context of the predicted structure for the related eubacterial apocarotenal oxygenase. ..
  75. Odenwald W, Rasband W, Kuzin A, Brody T. EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA. Proc Natl Acad Sci U S A. 2005;102:14700-5 pubmed publisher
    ..Also, evoprinter allows one to assess the degree of evolutionary divergence between orthologous DNAs by highlighting differences between a selected species and the other test species...
  76. Philibert R, King B, Winfield S, Cook E, Lee Y, Stubblefield B, et al. Association of an X-chromosome dodecamer insertional variant allele with mental retardation. Mol Psychiatry. 1998;3:303-9 pubmed
    ..001) and treatment with antidepressants (P < 0.001). We conclude that the presence of this 12-bp variant confers significant susceptibility for mental retardation. ..
  77. Strunnikov A, Aravind L, Koonin E. Saccharomyces cerevisiae SMT4 encodes an evolutionarily conserved protease with a role in chromosome condensation regulation. Genetics. 2001;158:95-107 pubmed
    ..The SIZ1 gene disruption is synthetically lethal with the SIZ2 deletion. We propose that SMT4, SIZ1, and SIZ2 are involved in a novel pathway of chromosome maintenance. ..
  78. McGlynn K, Hunter K, LeVoyer T, Roush J, Wise P, Michielli R, et al. Susceptibility to aflatoxin B1-related primary hepatocellular carcinoma in mice and humans. Cancer Res. 2003;63:4594-601 pubmed
    ..These results indicate that the comparison of results from human studies and the AFB(1)-susceptible mouse model may provide new insights into hepatocarcinogenesis. ..
  79. Muppidi J, Lobito A, Ramaswamy M, Yang J, Wang L, Wu H, et al. Homotypic FADD interactions through a conserved RXDLL motif are required for death receptor-induced apoptosis. Cell Death Differ. 2006;13:1641-50 pubmed
  80. Luk E, Vu N, Patteson K, Mizuguchi G, Wu W, Ranjan A, et al. Chz1, a nuclear chaperone for histone H2AZ. Mol Cell. 2007;25:357-68 pubmed
    ..The presence of this motif in other metazoan proteins suggests that H2AZ-specific chaperones may be widely conserved. ..
  81. Miles S, Carpenter B, Gancz H, Merrell D. Helicobacter pylori apo-Fur regulation appears unconserved across species. J Microbiol. 2010;48:378-86 pubmed publisher
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