Genomes and Genes
Experts and Doctors on adenosine triphosphate in Berkeley, California, United States
Locale: Berkeley, California, United States
Topic: adenosine triphosphate
- Lemon B, Inouye C, King D, Tjian R. Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature. 2001;414:924-8 pubmed..These studies demonstrate functional selectivity amongst highly related complexes involved in gene regulation and help define a more complete set of factors and cofactors required to activate transcription. ..
- Adelman J, Jeong Y, Liao J, Patel G, Kim D, Oster G, et al. Mechanochemistry of transcription termination factor Rho. Mol Cell. 2006;22:611-21 pubmed
- Jeruzalmi D, O Donnell M, Kuriyan J. Clamp loaders and sliding clamps. Curr Opin Struct Biol. 2002;12:217-24 pubmed..Crystallographic and electron microscopic views of clamp loaders from bacteria, archaebacteria and eukaryotes emphasize their common architecture and have produced models of how ATPbinding might be coupled to clamp opening/loading. ..
- Dose A, Hillman D, Wong C, Sohlberg L, Lin Jones J, Burnside B. Myo3A, one of two class III myosin genes expressed in vertebrate retina, is localized to the calycal processes of rod and cone photoreceptors and is expressed in the sacculus. Mol Biol Cell. 2003;14:1058-73 pubmed..The numerous IQ motifs may play a structural or signaling role in the Myo3A, and its localization to calycal processes indicates that this myosin mediates a local function at this site in vertebrate photoreceptors. ..
- Kelch B, Makino D, O Donnell M, Kuriyan J. How a DNA polymerase clamp loader opens a sliding clamp. Science. 2011;334:1675-80 pubmed publisher..The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA...
- Martin A, Welch M, Drubin D. Arp2/3 ATP hydrolysis-catalysed branch dissociation is critical for endocytic force generation. Nat Cell Biol. 2006;8:826-33 pubmed..Our results suggest a critical feature of dendritic nucleation in which debranching and subsequent actin-filament remodelling and/or depolymerization are important for endocytic vesicle morphogenesis. ..
- Corbett K, Benedetti P, Berger J. Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Nat Struct Mol Biol. 2007;14:611-9 pubmed publisher..These data afford important insights into the mechanisms of topo VI and related proteins, including type IIA topoisomerases and the Spo11 meiotic recombination endonuclease...
- Oster G, Wang H. Rotary protein motors. Trends Cell Biol. 2003;13:114-21 pubmed..Here, we review the current understanding of how these protein motors convert their energy supply into a rotary torque. ..
- Kim S, Shin D, Choi I, Schulze Gahmen U, Chen S, Kim R. Structure-based functional inference in structural genomics. J Struct Funct Genomics. 2003;4:129-35 pubmed
- Aathavan K, Politzer A, Kaplan A, Moffitt J, Chemla Y, Grimes S, et al. Substrate interactions and promiscuity in a viral DNA packaging motor. Nature. 2009;461:669-73 pubmed publisher..Such promiscuous, nonspecific contacts may reflect common translocase-substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily...
- Mimura C, Admon A, Hurt K, Ames G. The nucleotide-binding site of HisP, a membrane protein of the histidine permease. Identification of amino acid residues photoaffinity labeled by 8-azido-ATP. J Biol Chem. 1990;265:19535-42 pubmed..These consensus motifs are found in many purine nucleotide-binding proteins. The relationship between the location of these residues and the overall structure of the ATP-binding site is discussed...
- Williams T, Tjian R. Characterization of a dimerization motif in AP-2 and its function in heterologous DNA-binding proteins. Science. 1991;251:1067-71 pubmed..The resulting chimeric protein specifically recognized an AP-1 DNA-binding site in the absence of an intact c-Jun leucine repeat and in a manner that was dependent on the presence of a functional AP-2 dimerization domain. ..
- Van Dien S, Keasling J. Effect of polyphosphate metabolism on the Escherichia coli phosphate-starvation response. Biotechnol Prog. 1999;15:587-93 pubmed..The induction profiles resulting from the population-averaged values more closely matched experimental results than did those with the nonsegregated model. ..
- Thomsen N, Berger J. Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell. 2009;139:523-34 pubmed publisher..For a video summary of this article, see the PaperFlick file with the Supplemental Data available online. ..
- Martin A, Xu X, Rouiller I, Kaksonen M, Sun Y, Belmont L, et al. Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function. J Cell Biol. 2005;168:315-28 pubmed..These data demonstrate the importance of Arp2 and Arp3 nucleotide binding for nucleating activity, and Arp3 nucleotide binding for maintenance of cortical actin cytoskeleton cytoarchitecture. ..
- Näär A, Lemon B, Tjian R. Transcriptional coactivator complexes. Annu Rev Biochem. 2001;70:475-501 pubmed..The extent of functional interplay between these different activities in gene-specific transcriptional regulation is only now becoming apparent, and will remain an active area of research for years to come. ..
- Chesnokov I, Remus D, Botchan M. Functional analysis of mutant and wild-type Drosophila origin recognition complex. Proc Natl Acad Sci U S A. 2001;98:11997-2002 pubmed..Studies reported here provide the first functional dissection of a metazoan initiator and highlight the basic conserved and divergent features among Drosophila and budding yeast ORC complexes. ..
- Strycharska M, Arias Palomo E, Lyubimov A, Erzberger J, O Shea V, BUSTAMANTE C, et al. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell. 2013;52:844-54 pubmed publisher..Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors. ..
- Greber B, Nguyen T, Fang J, Afonine P, Adams P, Nogales E. The cryo-electron microscopy structure of human transcription factor IIH. Nature. 2017;549:414-417 pubmed publisher..Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity. ..
- Liu J, Lou Y, Yokota H, Adams P, Kim R, Kim S. Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol. 2005;354:289-303 pubmed publisher..A possible phosphate transfer mechanism is proposed on the basis of the structures presented...
- Carroll J, Munchel S, Weis K. The DExD/H box ATPase Dhh1 functions in translational repression, mRNA decay, and processing body dynamics. J Cell Biol. 2011;194:527-37 pubmed publisher..Our results place Dhh1 at the interface of translation and decay controlling whether an mRNA is translated, stored, or decayed. ..
- Kazmirski S, Podobnik M, Weitze T, O Donnell M, Kuriyan J. Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex. Proc Natl Acad Sci U S A. 2004;101:16750-5 pubmed
- Zarembinski T, Hung L, Mueller Dieckmann H, Kim K, Yokota H, Kim R, et al. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci U S A. 1998;95:15189-93 pubmed..This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics...
- Zhang Y, Smith C, Saha A, Grill S, Mihardja S, Smith S, et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006;24:559-68 pubmed..Such loop formation may provide a molecular basis for the biological functions of remodelers. ..
- Kobor M, Venkatasubrahmanyam S, Meneghini M, Gin J, Jennings J, Link A, et al. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004;2:E131 pubmed..Metazoan orthologs of Swr1p (Drosophila Domino; human SRCAP and p400) may have analogous functions...
- Remus D, Blanchette M, Rio D, Botchan M. CDK phosphorylation inhibits the DNA-binding and ATP-hydrolysis activities of the Drosophila origin recognition complex. J Biol Chem. 2005;280:39740-51 pubmed..These results suggest molecular mechanisms by which Cdks may inhibit ORC function as part of re-replication control and show that DmORC activity may be modulated in response to phosphorylation by multiple kinases. ..
- Peters T, Miller A, Tourette C, Agren H, Hubbard A, Hughes R. Genomic Analysis of ATP Efflux in Saccharomyces cerevisiae. G3 (Bethesda). 2015;6:161-70 pubmed publisher..These results will facilitate analysis of ATP efflux mechanisms in higher eukaryotes. ..
- Rybenkov V, Ullsperger C, Vologodskii A, Cozzarelli N. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science. 1997;277:690-3 pubmed..The results imply that type II topoisomerases use the energy of adenosine triphosphate hydrolysis to preferentially remove the topological links that provide barriers to DNA segregation. ..
- Young T, Delagoutte B, Endrizzi J, Falick A, Alber T. Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases. Nat Struct Biol. 2003;10:168-74 pubmed..The structural and chemical similarities of PknB to metazoan homologs support a universal activation mechanism of Ser/Thr protein kinases in prokaryotes and eukaryotes. ..
- Nollmann M, Stone M, Bryant Z, Gore J, Crisona N, Hong S, et al. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol. 2007;14:264-71 pubmed..A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data. ..
- Bergeron L, Tokatlian T, Gomez L, Clark D. Redirecting the inactivation pathway of penicillin amidase and increasing amoxicillin production via a thermophilic molecular chaperone. Biotechnol Bioeng. 2009;102:417-24 pubmed publisher..The thermosome and other thermophilic chaperones may thus be generally useful for stabilizing enzymes in their soluble form and expanding the range of conditions suitable for biocatalysis. ..
- Crisona N, Cozzarelli N. Alteration of Escherichia coli topoisomerase IV conformation upon enzyme binding to positively supercoiled DNA. J Biol Chem. 2006;281:18927-32 pubmed..We suggest that the altered conformation reflects efficient binding by topo IV of the two DNA segments that participate in the strand passage reaction. ..
- Carmen R, Sohmer P, Leng B, Moore G, Nelson E, Simon T, et al. Five-week red cell storage with preservation of 2,3 DPG. Transfusion. 1988;28:157-61 pubmed..8 and 74.1 percent after 4 and 5 weeks of storage, respectively. The AS-4 system provides a red cell product with acceptable viability and improved oxygen off-loading function. ..
- Dean D, Davidson A, Nikaido H. The role of ATP as the energy source for maltose transport in Escherichia coli. Res Microbiol. 1990;141:348-52 pubmed
- Elston T, Wang H, Oster G. Energy transduction in ATP synthase. Nature. 1998;391:510-3 pubmed..Moreover, the motor's reversibility-supplying torque from ATP hydrolysis in F1 converts the motor into an efficient proton pump-can also be explained by our model. ..
- Corbett K, Berger J. Structure of the ATP-binding domain of Plasmodium falciparum Hsp90. Proteins. 2010;78:2738-44 pubmed publisher..Our results should aid in the structural understanding of Hsp90-drug interactions in P. falciparum, and provide a scaffold for future drug-discovery efforts...
- Keener J, Kustu S. Protein kinase and phosphoprotein phosphatase activities of nitrogen regulatory proteins NTRB and NTRC of enteric bacteria: roles of the conserved amino-terminal domain of NTRC. Proc Natl Acad Sci U S A. 1988;85:4976-80 pubmed..A purified amino-terminal fragment of NTRC (approximately equal to 12.5 kDa) is sufficient for recognition by NTRB and is autodephosphorylated at the same rate as the native protein. ..
- Mempin R, Tran H, Chen C, Gong H, Kim Ho K, Lu S. Release of extracellular ATP by bacteria during growth. BMC Microbiol. 2013;13:301 pubmed publisher..Our results indicate that extracellular ATP is produced by many bacterial species during growth and extracellular ATP may serve a role in the bacterial physiology. ..
- Hardy C, Cozzarelli N. Alteration of Escherichia coli topoisomerase IV to novobiocin resistance. Antimicrob Agents Chemother. 2003;47:941-7 pubmed..We conclude that topo IV is a secondary target of novobiocin and that it is very likely to be inhibited by the same mechanism as DNA gyrase. ..
- Madiraju M, Clark A. Effect of RecF protein on reactions catalyzed by RecA protein. Nucleic Acids Res. 1991;19:6295-300 pubmed..We found that it required a much higher ratio of RecF to RecA protein than normally occurs in vivo to inhibit joint molecule formation. The insight that these data give to the normal functioning of RecF protein is discussed. ..
- Goedken E, Levitus M, Johnson A, Bustamante C, O Donnell M, Kuriyan J. Fluorescence measurements on the E.coli DNA polymerase clamp loader: implications for conformational changes during ATP and clamp binding. J Mol Biol. 2004;336:1047-59 pubmed
- Kuchler K, Dohlman H, Thorner J. The a-factor transporter (STE6 gene product) and cell polarity in the yeast Saccharomyces cerevisiae. J Cell Biol. 1993;120:1203-15 pubmed
- Reindl S, Ghosh A, Williams G, Lassak K, Neiner T, Henche A, et al. Insights into FlaI functions in archaeal motor assembly and motility from structures, conformations, and genetics. Mol Cell. 2013;49:1069-82 pubmed publisher..Collective structural and mutational results identify in vivo functional components for assembly and motility, phosphate-triggered rearrangements by ATP hydrolysis, and molecular predictors for distinct ATPase superfamily functions...
- Ilves I, Petojevic T, Pesavento J, Botchan M. Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol Cell. 2010;37:247-58 pubmed publisher..The onset of DNA replication and unwinding may thus occur through allosteric changes in MCM2-7 affected by the association of these ancillary factors. ..
- Peterson M, Inostroza J, Maxon M, Flores O, Admon A, Reinberg D, et al. Structure and functional properties of human general transcription factor IIE. Nature. 1991;354:369-73 pubmed..Analysis of their predicted amino-acid sequences reveals several intriguing structural motifs that could provide insight into the role of TFIIE in transcription initiation. ..
- Yu J, Cheng W, Bustamante C, Oster G. Coupling translocation with nucleic acid unwinding by NS3 helicase. J Mol Biol. 2010;404:439-55 pubmed publisher..The generic features of coupling single-stranded nucleic acid translocation with duplex unwinding presented in this work may apply generally to a class of helicases. ..
- Belotserkovskii B, Arimondo P, Cozzarelli N. Topoisomerase action on short DNA duplexes reveals requirements for gate and transfer DNA segments. J Biol Chem. 2006;281:25407-15 pubmed..Topo IV cleaved the DNA-DNA duplex, but not the DNA-RNA duplex implying that the DNA-RNA duplex can be a T-segment but not a G-segment. ..
- Nollmann M, Crisona N, Arimondo P. Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie. 2007;89:490-9 pubmed..Here, we review the biological roles of gyrase in vivo and its mechanism in vitro. ..
- Hall J, Ganesan A, Chen J, Nikaido H. Two modes of ligand binding in maltose-binding protein of Escherichia coli. Functional significance in active transport. J Biol Chem. 1997;272:17615-22 pubmed
- Belmont L, Drubin D. The yeast V159N actin mutant reveals roles for actin dynamics in vivo. J Cell Biol. 1998;142:1289-99 pubmed..Analysis of the cables in these double-mutant cells supports a role for fimbrin in organizing cytoplasmic cables and for Mdm20p and tropomyosin in excluding cofilin from the cables. ..
- Davidson A, Shuman H, Nikaido H. Mechanism of maltose transport in Escherichia coli: transmembrane signaling by periplasmic binding proteins. Proc Natl Acad Sci U S A. 1992;89:2360-4 pubmed
- Xing J, Wang H, von Ballmoos C, Dimroth P, Oster G. Torque generation by the Fo motor of the sodium ATPase. Biophys J. 2004;87:2148-63 pubmed..This work also illustrates how to extract a motor mechanism from dynamical experimental observations in the absence of complete structural information...
- Lander G, Estrin E, Matyskiela M, Bashore C, Nogales E, Martin A. Complete subunit architecture of the proteasome regulatory particle. Nature. 2012;482:186-91 pubmed publisher..We provide a structural basis for the ability of the proteasome to degrade a diverse set of substrates and thus regulate vital cellular processes. ..
- Wang H, Oster G. Energy transduction in the F1 motor of ATP synthase. Nature. 1998;396:279-82 pubmed
- Erzberger J, Mott M, Berger J. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol. 2006;13:676-83 pubmed publisher..Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly forms the core element of initiators in all domains of life...
- Clarey M, Erzberger J, Grob P, Leschziner A, Berger J, Nogales E, et al. Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. Nat Struct Mol Biol. 2006;13:684-90 pubmed..By analogy to the DNA-wrapping activity of DnaA, we posit that ORC together with Cdc6 prepares origin DNA for helicase loading through mechanisms related to the established pathway of prokaryotes. ..
- Davidson A, Nikaido H. Overproduction, solubilization, and reconstitution of the maltose transport system from Escherichia coli. J Biol Chem. 1990;265:4254-60 pubmed..These results provide strong evidence that it is the hydrolysis of ATP by a component of the transport complex that provides the energy required for active maltose transport...
- Custer A. Stoichiometric estimates of the biochemical conversion efficiencies in tsetse metabolism. BMC Ecol. 2005;5:6 pubmed..These results now enable a deeper analysis of tsetse ecology based on the construction of a dynamic mass-energy budget for tsetse and their populations. ..
- Ranatunga W, Hill E, Mooster J, Holbrook E, Schulze Gahmen U, Xu W, et al. Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. J Mol Biol. 2004;339:103-16 pubmed publisher..The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved...
- Simonetta K, Kazmirski S, Goedken E, Cantor A, Kelch B, McNally R, et al. The mechanism of ATP-dependent primer-template recognition by a clamp loader complex. Cell. 2009;137:659-71 pubmed publisher..By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex. ..
- Lyman S, Schekman R. Binding of secretory precursor polypeptides to a translocon subcomplex is regulated by BiP. Cell. 1997;88:85-96 pubmed..This release reaction, which is specific to BiP and requires interaction between BiP and the DnaJ homolog Sec63p, defines a role for BiP and Sec63p early in the ER translocation process. ..