Genomes and Genes
Experts and Doctors on conserved sequence in Denmark
Topic: conserved sequence
- Hansen M, Nielsen J, Retelska D, Larsen N, Leffers H. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. Mol Reprod Dev. 2008;75:219-29 pubmed..Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths. ..
- Fredslund J, Madsen L, Hougaard B, Nielsen A, Bertioli D, Sandal N, et al. A general pipeline for the development of anchor markers for comparative genomics in plants. BMC Genomics. 2006;7:207 pubmed..Based on this database, we have evaluated 76 candidate anchor loci with respect to marker development in legume species with no sequence information available, demonstrating the validity of this approach. ..
- Pedersen G, Rattenborg T, Knudsen C, Clark B. The role of Glu259 in Escherichia coli elongation factor Tu in ternary complex formation. Protein Eng. 1998;11:101-8 pubmed
- Hobolth A, Dutheil J, Hawks J, Schierup M, Mailund T. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res. 2011;21:349-56 pubmed publisher..Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny. ..
- Larsen K, Madsen L, Bendixen C. Porcine SPLUNC1: molecular cloning, characterization and expression analysis. Biochim Biophys Acta. 2005;1727:220-6 pubmed..This airway-specific expression might be of particular interest in the study of airborne diseases in pig. ..
- Struve C, Bojer M, Krogfelt K. Identification of a conserved chromosomal region encoding Klebsiella pneumoniae type 1 and type 3 fimbriae and assessment of the role of fimbriae in pathogenicity. Infect Immun. 2009;77:5016-24 pubmed publisher..pneumoniae infections. However, since type 3 fimbriae promote biofilm formation, their role in development of infections in catheterized patients needs to be elucidated. ..
- Piskur J, Sandrini M, Knecht W, Munch Petersen B. Animal deoxyribonucleoside kinases: 'forward' and 'retrograde' evolution of their substrate specificity. FEBS Lett. 2004;560:3-6 pubmed..Thereafter, insects lost all but one kinase, dNK (EC 22.214.171.124), which subsequently, through remodelling of a limited number of amino acid residues, gained a broad substrate specificity. ..
- Godfrey D, Böhlenius H, Pedersen C, Zhang Z, Emmersen J, Thordal Christensen H. Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif. BMC Genomics. 2010;11:317 pubmed publisher..All together, our findings suggest the Y/F/WxC-proteins to be a new class of effectors from haustoria-producing pathogenic fungi. ..
- Wolf X, Serup P, Hyttel P. Three-dimensional immunohistochemical characterization of lineage commitment by localization of T and FOXA2 in porcine peri-implantation embryos. Dev Dyn. 2011;240:890-7 pubmed publisher..In all developmental stages, FOXA2 was expressed in the entire hypoblast/definitive endoderm. We conclude that the expression pattern of T and FOXA2 is largely conserved between pig and mouse. ..
- Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup F, Ussery D. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012;13:88 pubmed publisher..Identification of genes with different degrees of variation is important especially in trend analysis. ..
- de Diego I, Ksiazek M, Mizgalska D, Koneru L, Golik P, Szmigielski B, et al. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal ?-sandwich domain. Sci Rep. 2016;6:23123 pubmed publisher..These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway. ..
- Vestergaard G, Aramayo R, Basta T, Häring M, Peng X, Brugger K, et al. Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. J Virol. 2008;82:371-81 pubmed
- Seemann S, Richter A, Gesell T, Backofen R, Gorodkin J. PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics. 2011;27:211-9 pubmed publisher..We observed increased performance with increased amounts of covariance. The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold. ..
- Kjaergaard M, Hansen L, Jacobsen B, Gardsvoll H, Ploug M. Structure and ligand interactions of the urokinase receptor (uPAR). Front Biosci. 2008;13:5441-61 pubmed..The structural biology of uPAR will be reviewed with special emphasis on its multidomain composition and the interaction with its natural protein ligands, i.e. the serine protease uPA and the matrix protein vitronectin. ..
- Rasmussen S, Mikkelsen J, Pedersen F. Modulation of homo- and heterodimerization of Harvey sarcoma virus RNA by GACG tetraloops and point mutations in palindromic sequences. J Mol Biol. 2002;323:613-28 pubmed..The complementarity of loop sequences in the packaging signal upstream of the GACG tetraloops might therefore determine homo- and heterodimerization specificity and recombination activity of these viruses...
- Clausen J, Vilsen B, McIntosh D, Einholm A, Andersen J. Glutamate-183 in the conserved TGES motif of domain A of sarcoplasmic reticulum Ca2+-ATPase assists in catalysis of E2/E2P partial reactions. Proc Natl Acad Sci U S A. 2004;101:2776-81 pubmed
- Friis Nielsen J, KjartansdÃ³ttir K, Mollerup S, Asplund M, Mourier T, Jensen R, et al. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses. 2016;8: pubmed publisher..Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified. ..
- Kostenis E, Martini L, Ellis J, Waldhoer M, Heydorn A, Rosenkilde M, et al. A highly conserved glycine within linker I and the extreme C terminus of G protein alpha subunits interact cooperatively in switching G protein-coupled receptor-to-effector specificity. J Pharmacol Exp Ther. 2005;313:78-87 pubmed
- Schwer B, Bunkenborg J, Verdin R, Andersen J, Verdin E. Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2. Proc Natl Acad Sci U S A. 2006;103:10224-10229 pubmed publisher..Because the activity of a bacterial ortholog of AceCS2, called ACS, is controlled via deacetylation by a bacterial sirtuin protein, our observation highlights the conservation of a metabolic regulatory pathway from bacteria to humans. ..
- Rosenkilde M, Kledal T, Schwartz T. High constitutive activity of a virus-encoded seven transmembrane receptor in the absence of the conserved DRY motif (Asp-Arg-Tyr) in transmembrane helix 3. Mol Pharmacol. 2005;68:11-9 pubmed..It is concluded that the Arg of the DRY motif in transmembrane helix 3 is not essential for G protein coupling based on the constitutive as well as the ligand-mediated activity observed for ORF74-EHV2. ..
- Frodin M, Antal T, Dummler B, Jensen C, Deak M, Gammeltoft S, et al. A phosphoserine/threonine-binding pocket in AGC kinases and PDK1 mediates activation by hydrophobic motif phosphorylation. EMBO J. 2002;21:5396-407 pubmed..Sequence conservation suggests that this mechanism is a key feature in activation of >40 human AGC kinases. ..
- Bottger P, Pedersen L. Two highly conserved glutamate residues critical for type III sodium-dependent phosphate transport revealed by uncoupling transport function from retroviral receptor function. J Biol Chem. 2002;277:42741-7 pubmed..Finally, the results also show that Pit2 retroviral receptor function per se is not dependent on Pit2 P(i) transport function. ..
- Kjaerulff S, Davey J, Nielsen O. Analysis of the structural genes encoding M-factor in the fission yeast Schizosaccharomyces pombe: identification of a third gene, mfm3. Mol Cell Biol. 1994;14:3895-905 pubmed..Additionally, the signal transduction machinery associated with the pheromone response is required for transcription of the mfm genes in both stimulated and unstimulated cells. ..
- Hansen K, Hauser F, Cazzamali G, Williamson M, Grimmelikhuijzen C. Cloning and characterization of the adipokinetic hormone receptor from the cockroach Periplaneta americana. Biochem Biophys Res Commun. 2006;343:638-43 pubmed publisher..This paper describes the first AKH receptor from a hemimetabolous insect...
- Kristensen O, Ross B, Gajhede M. Structure of the PPX/GPPA phosphatase from Aquifex aeolicus in complex with the alarmone ppGpp. J Mol Biol. 2008;375:1469-76 pubmed publisher..The arginines R22 and R267, residing in different domains, are crucial for guanosine pentaphosphate specificity as they interact with the unique 3'-ribose phosphorylation...
- Pedersen K, Finsen B, Celis J, Jensen N. Expression of a novel murine phospholipase D homolog coincides with late neuronal development in the forebrain. J Biol Chem. 1998;273:31494-504 pubmed
- Sajid W, Kulahin N, Schluckebier G, Ribel U, Henderson H, Tatar M, et al. Structural and biological properties of the Drosophila insulin-like peptide 5 show evolutionary conservation. J Biol Chem. 2011;286:661-73 pubmed publisher..DILP5 also binds to insect insulin-binding proteins. These results show high evolutionary conservation of the insulin receptor binding properties despite divergent insulin dimerization mechanisms. ..
- Christiansen M, Stevnsner T, Modin C, Martensen P, Brosh R, Bohr V. Functional consequences of mutations in the conserved SF2 motifs and post-translational phosphorylation of the CSB protein. Nucleic Acids Res. 2003;31:963-73 pubmed..These observations may have significant implications for the function of CSB in vivo. ..
- Damgaard C, Tange T, Kjems J. hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure. RNA. 2002;8:1401-15 pubmed
- Nielsen A, Oulad Abdelghani M, Ortiz J, Remboutsika E, Chambon P, Losson R. Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol Cell. 2001;7:729-39 pubmed..These results define a novel function for the conserved CD and suggest that HP1 self-association and histone binding may play a crucial role in HP1-mediated heterochromatin assembly. ..
- Sørensen C, Lukas C, Kramer E, Peters J, Bartek J, Lukas J. A conserved cyclin-binding domain determines functional interplay between anaphase-promoting complex-Cdh1 and cyclin A-Cdk2 during cell cycle progression. Mol Cell Biol. 2001;21:3692-703 pubmed..Collectively, these data provide a mechanistic explanation for the mutual functional interplay between cyclin A-Cdk2 and APC-Cdh1 and the first evidence that Cdh1 may activate the APC by binding specific substrates. ..
- Andersen G, Thirup S, Spremulli L, Nyborg J. High resolution crystal structure of bovine mitochondrial EF-Tu in complex with GDP. J Mol Biol. 2000;297:421-36 pubmed..The C-terminal extension of mitochondrial EF-Tu has structural similarities with DNA recognising zinc fingers suggesting that the extension may be involved in recognition of RNA. ..
- Wadskov Hansen S, Martinussen J, Hammer K. The pyrH gene of Lactococcus lactis subsp. cremoris encoding UMP kinase is transcribed as part of an operon including the frr1 gene encoding ribosomal recycling factor 1. Gene. 2000;241:157-66 pubmed..lactis shows a high resemblance to that found in Bacillus subtilis as well as in Escherichia coli and several other prokaryotes ..
- Nørholm A, Hendus Altenburger R, Bjerre G, Kjaergaard M, Pedersen S, Kragelund B. The intracellular distal tail of the Na+/H+ exchanger NHE1 is intrinsically disordered: implications for NHE1 trafficking. Biochemistry. 2011;50:3469-80 pubmed publisher..We suggest that normal NHE1 function depends on a protein recognition element within the ID region that may be linked to NHE1 trafficking via an acidic ER export motif. ..
- Bennett E, Chen Y, Schwientek T, Mandel U, Schjoldager K, Cohen S, et al. Rescue of Drosophila Melanogaster l(2)35Aa lethality is only mediated by polypeptide GalNAc-transferase pgant35A, but not by the evolutionary conserved human ortholog GalNAc-transferase-T11. Glycoconj J. 2010;27:435-44 pubmed publisher
- Hundahl C, Fago A, Dewilde S, Moens L, Hankeln T, Burmester T, et al. Oxygen binding properties of non-mammalian nerve globins. FEBS J. 2006;273:1323-9 pubmed..These results demonstrate a remarkable diversity in oxygenation characteristics of vertebrate and invertebrate nerve haemoglobins that clearly reflect distinct physiological roles. ..
- Schwientek T, Bennett E, Flores C, Thacker J, Hollmann M, Reis C, et al. Functional conservation of subfamilies of putative UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases in Drosophila, Caenorhabditis elegans, and mammals. One subfamily composed of l(2)35Aa is essential in Drosophila. J Biol Chem. 2002;277:22623-38 pubmed
- Nielsen J, B ggild A, Andersen C, Nielsen G, Boysen A, Brodersen D, et al. An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii. RNA. 2007;13:2213-23 pubmed publisher..Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable...
- Purta E, O Connor M, Bujnicki J, Douthwaite S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol. 2009;72:1147-58 pubmed publisher..The ygdE gene has been redesignated rlmM for rRNA large subunit methyltransferase M. ..
- Graversen J, Madsen M, Moestrup S. CD163: a signal receptor scavenging haptoglobin-hemoglobin complexes from plasma. Int J Biochem Cell Biol. 2002;34:309-14 pubmed..The novel functional linkage of CD163 and Hp, which both are induced during inflammation, also reveal some interesting perspectives relating to the suggested anti-inflammatory properties of the receptor and the Hp phenotypes. ..
- Eckert Boulet N, Lisby M. Regulation of homologous recombination at telomeres in budding yeast. FEBS Lett. 2010;584:3696-702 pubmed publisher..Here, we review the mechanisms that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae. ..
- Gjetting T, Petersen M, Guldberg P, Guttler F. Missense mutations in the N-terminal domain of human phenylalanine hydroxylase interfere with binding of regulatory phenylalanine. Am J Hum Genet. 2001;68:1353-60 pubmed
- Minocherhomji S, Seemann S, Mang Y, El Schich Z, Bak M, Hansen C, et al. Sequence and expression analysis of gaps in human chromosome 20. Nucleic Acids Res. 2012;40:6660-72 pubmed..Four ncRNAs expressed within the gap at DLGAP4 show elevated expression in the human brain. Our data suggest that unfinished human genome gaps are likely to comprise numerous functional elements. ..
- Jank T, Belyi Y, Wirth C, Rospert S, Hu Z, Dengjel J, et al. Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A. J Biol Chem. 2017;292:16014-16023 pubmed publisher..We therefore conclude that eEF1A glutaminylation is a yeast-specific posttranslational modification that appears to influence protein translation. ..
- Cazzamali G, Klaerke D, Grimmelikhuijzen C. A new family of insect tyramine receptors. Biochem Biophys Res Commun. 2005;338:1189-96 pubmed publisher..The Drosophila tyramine receptor is, to our knowledge, the first cloned insect G protein-coupled receptor that appears to be fully specific for tyramine...
- Lykke Andersen J, Garrett R. RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history. EMBO J. 1997;16:6290-300 pubmed publisher..jannaschii enzyme consists of two isologously associated dimers, each similar to one H.volcanii monomer and each consisting of two monomers, where one face of monomer 1 and the opposite face of monomer 2 are involved in RNA binding...
- Frimurer T, Bywater R. Structure of the integral membrane domain of the GLP1 receptor. Proteins. 1999;35:375-86 pubmed
- Poulsen H, Nilsson J, Damgaard C, Egebjerg J, Kjems J. CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain. Mol Cell Biol. 2001;21:7862-71 pubmed..Furthermore, our data imply that nuclear import of (i)ADAR1 is mediated by at least two nuclear localization sequences. These results suggest that the nuclear editing activity of (i)ADAR1 is modulated by nuclear export. ..
- Kilian M, Poulsen K, Lomholt H. Evolution of the paralogous hap and iga genes in Haemophilus influenzae: evidence for a conserved hap pseudogene associated with microcolony formation in the recently diverged Haemophilus aegyptius and H. influenzae biogroup aegyptius. Mol Microbiol. 2002;46:1367-80 pubmed..aegyptius and H. influenzae biogroup aegyptius occurred subsequent to this genetic event. The loss of Hap protein expression may be one of the genetic events that facilitated exploitation of the conjunctivae as a new niche...
- Vestergaard B, Van L, Andersen G, Nyborg J, Buckingham R, Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol Cell. 2001;8:1375-82 pubmed
- Andersen C, Torvund Jensen M, Nielsen M, de Oliveira C, Hersleth H, Andersen N, et al. Structure of the haptoglobin-haemoglobin complex. Nature. 2012;489:456-9 pubmed publisher..Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of multimeric haptoglobin-haemoglobin for CD163 (ref. 4)...
- Blechingberg J, Holm I, Nielsen A. Characterization and expression analysis in the developing embryonic brain of the porcine FET family: FUS, EWS, and TAF15. Gene. 2012;493:27-35 pubmed publisher..The presented results indicate that the porcine brain could be an alternative model for the future examination of the normal functions as well as neurological disease associated functions of the FET proteins...
- Andersen K, Nielsen H. Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila. Nucleic Acids Res. 2012;40:1267-81 pubmed publisher..Further, we found a candidate for the first U8 outside metazoans, and an unusual U14 candidate. In addition, a number of candidates for new non-coding RNAs were characterized by expression analysis at different growth conditions...
- Lehnherr H, Bendtsen J, Preuss F, Ilyina T. Identification and characterization of the single-stranded DNA-binding protein of bacteriophage P1. J Bacteriol. 1999;181:6463-8 pubmed..However, the close relationship between SSB-P1 and the SSB protein of the P1 host, E. coli, raises questions about the functional significance of the phage protein...
- Knudsen B, Miyamoto M, Laipis P, Silverman D. Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases. Genetics. 2003;164:1261-9 pubmed..As illustrated by the CAs, these LRTs, in combination with other biological evidence, offer a powerful and cost-effective approach for testing hypotheses, making predictions, and designing experiments in protein functional studies. ..
- Valentin Hansen P, Eriksen M, Udesen C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol. 2004;51:1525-33 pubmed..Here, we summarize the history of Hfq and highlight results that have led to an important gain in insight into the physiology, biochemistry and evolution of Hfq and its homologues. ..
- Larsen K, Madsen L. Sequence conservation between porcine and human LRRK2. Mol Biol Rep. 2009;36:237-43 pubmed..The porcine LRRK2 gene was mapped to chromosome 5q25. The results obtained suggest that the LRRK2 gene might be of particular interest in our attempt to generate a transgenic porcine model for Parkinson's disease. ..
- Bøttger P, Pedersen L. Evolutionary and experimental analyses of inorganic phosphate transporter PiT family reveals two related signature sequences harboring highly conserved aspartic acids critical for sodium-dependent phosphate transport function of human PiT2. FEBS J. 2005;272:3060-74 pubmed..The present data are in agreement with a possible role of the signature sequences in translocation of cations. ..
- Frolova L, Le Goff X, Rasmussen H, Cheperegin S, Drugeon G, Kress M, et al. A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature. 1994;372:701-3 pubmed publisher..The amino-acid sequence of the eRF1 family is highly conserved. We conclude that the eRF1 proteins are directly implicated in the termination of translation in eukaryotes...
- Sørensen E, Højrup P, Petersen T. Posttranslational modifications of bovine osteopontin: identification of twenty-eight phosphorylation and three O-glycosylation sites. Protein Sci. 1995;4:2040-9 pubmed..This conservation of serines, even in otherwise less well-conserved regions of the protein, indicates that the phosphorylation of osteopontin at specific sites is essential for the function of the protein. ..
- Hjulsager C, Olsen B, Jensen D, Cordea M, Krath B, Johansen I, et al. Multiple determinants in the coding region of Pea seed-borne mosaic virus P3 are involved in virulence against sbm-2 resistance. Virology. 2006;355:52-61 pubmed publisher..Our findings comply with a model for PSbMV pathotypes having evolved by a diversification of the P3 protein likely to extend to the level of function...
- Bjornberg O, Grüner A, Roepstorff P, Jensen K. The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry. 1999;38:2899-908 pubmed..The S175C mutant was also defective with respect to substrate and product binding. Structural and mechanistic differences between the two different families of dihydroorotate dehydrogenase are discussed. ..
- Borg S, Poulsen C. Molecular analysis of two Ypt/Rab-related sequences isolated from soybean (Glycine max) DNA libraries. Plant Mol Biol. 1994;26:175-87 pubmed..The classification of the gmr sequences as relatives of the Ypt/Rab family suggests that the deduced GMR proteins are involved in control of processes related to vesicle trafficking in plant cells. ..
- Nielsen A, Jørgensen P, Lerouge T, Cerviño M, Chambon P, Losson R. Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. Mol Cell Biol. 2004;24:5184-96 pubmed..Thus, Nizp1 contains a novel type of zinc finger motif that functions as a docking site for NSD1 and is more than just a degenerate evolutionary remnant of a C2H2 motif. ..
- Gorodkin J, Hofacker I, Torarinsson E, Yao Z, Havgaard J, Ruzzo W. De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol. 2010;28:9-19 pubmed publisher..This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist. ..
- Schauser L, Wieloch W, Stougaard J. Evolution of NIN-like proteins in Arabidopsis, rice, and Lotus japonicus. J Mol Evol. 2005;60:229-37 pubmed publisher..Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide...
- Fredsted T, Villessen P. Fast and reliable sexing of prosimian and human DNA. Am J Primatol. 2004;64:345-50 pubmed..A single PCR yields two fragments in males and only one in females, which are easily separated with the use of agarose gels. Amplification of separable fragments was successful in seven species of lemurs, as well as humans...
- Dons L, Rasmussen O, Olsen J. Cloning and characterization of a gene encoding flagellin of Listeria monocytogenes. Mol Microbiol. 1992;6:2919-29 pubmed..monocytogenes can be divided into two groups. These groups correspond to the flagellar antigens AB and ABC, respectively, as well as to the two types of L. monocytogenes based on the DNA sequence of the listeriolysin gene. ..
- Ernst H, Lo Leggio L, Willemo s M, Leonard G, Blum P, Larsen S. Structure of the Sulfolobus solfataricus alpha-glucosidase: implications for domain conservation and substrate recognition in GH31. J Mol Biol. 2006;358:1106-24 pubmed publisher..It reveals Arg400, Asp87, Trp284, Met321 and Phe327 as invariant residues forming the +1 subsite in the GH31 alpha-glucosidases. Structural comparisons with other GH families suggest that the GH31 enzymes belong to clan GH-D...
- Steffensen S, Poulsen A, Mortensen K, Sperling Petersen H. E. coli translation initiation factor IF2--an extremely conserved protein. Comparative sequence analysis of the infB gene in clinical isolates of E. coli. FEBS Lett. 1997;419:281-4 pubmed..This Gln/Gly490 is located within the central GTP/GDP-binding domain IV of IF2. The results are further evidence that IF2 from E. coli has reached a highly defined level of structural and functional development. ..
- Hjelmsoe I, Allen C, Cohn M, Tulchinsky E, Wu L. The kappaB and V(D)J recombination signal sequence binding protein KRC regulates transcription of the mouse metastasis-associated gene S100A4/mts1. J Biol Chem. 2000;275:913-20 pubmed..These data indicate that KRC positively regulates transcription of S100A4/mts1. ..
- Poulsen S, Kofoed C, Vester B. Inhibition of the ribosomal peptidyl transferase reaction by the mycarose moiety of the antibiotics carbomycin, spiramycin and tylosin. J Mol Biol. 2000;304:471-81 pubmed
- Purta E, Kaminska K, Kasprzak J, Bujnicki J, Douthwaite S. YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA. 2008;14:2234-44 pubmed publisher..Methylation by YbeA (redesignated RlmH for rRNA large subunit methyltransferase H) possibly functions as a stamp of approval signifying that the 50S subunit has engaged in translational initiation. ..
- Laursen B, Kjaergaard A, Mortensen K, Hoffman D, Sperling Petersen H. The N-terminal domain (IF2N) of bacterial translation initiation factor IF2 is connected to the conserved C-terminal domains by a flexible linker. Protein Sci. 2004;13:230-9 pubmed..The features of structurally well-ordered N- and C-terminal domains connected by a flexible linker with significant helical content are reminiscent of another translation initiation factor, IF3. ..
- Larsen J, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen J. Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia. BMC Evol Biol. 2007;7:184 pubmed..We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data...
- Sørensen H, Hedegaard J, Sperling Petersen H, Mortensen K. Remarkable conservation of translation initiation factors: IF1/eIF1A and IF2/eIF5B are universally distributed phylogenetic markers. IUBMB Life. 2001;51:321-7 pubmed..Because of these two application levels, IF1/eIF1A-IF2/eIF5B is a phylogenetic "dual level" marker. ..
- Burton M, Rose T, Faergeman N, Knudsen J. Evolution of the acyl-CoA binding protein (ACBP). Biochem J. 2005;392:299-307 pubmed..The appearance of ACBP very early on in evolution points towards a fundamental role of ACBP in acyl-CoA metabolism, including ceramide synthesis and in signalling. ..
- Badsberg U, Jørgensen A, Gesmar H, Led J, Hammerstad J, Jespersen L, et al. Solution structure of reduced plastocyanin from the blue-green alga Anabaena variabilis. Biochemistry. 1996;35:7021-31 pubmed..v.PCu, is the main reason for the failure of the remote site of this plastocyanin to function as a significant electron transfer site. ..
- Hansen K, Ibarra P, Thon G. Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res. 2006;34:78-88 pubmed..The tlh genes are found in the subtelomeric regions of several other fungi raising the intriguing possibility of conserved regulation and function. ..
- Larsen M, Elfving B, Wiborg O. The chicken serotonin transporter discriminates between serotonin-selective reuptake inhibitors. A species-scanning mutagenesis study. J Biol Chem. 2004;279:42147-56 pubmed..Consequently, we suggest that Ala(169) and Ile(172) of human SERT are important residues in sensing the N-methylation state of SERT antagonists. ..
- Laursen B, Mortensen K, Sperling Petersen H, Hoffman D. A conserved structural motif at the N terminus of bacterial translation initiation factor IF2. J Biol Chem. 2003;278:16320-8 pubmed..The results of the present work will provide guidance for the design of future experiments directed toward understanding the functional roles of this widely conserved structural domain within IF2. ..