Aquifex aeolicus VF5

Summary

Alias: Aquifex aeolicus str. VF5

Top Publications

  1. Mauris J, Evans T. Adenosine triphosphate stimulates Aquifex aeolicus MutL endonuclease activity. PLoS ONE. 2009;4:e7175 pubmed publisher
    ..Finally, the C-terminal 123 amino acid residues of Aae MutL were sufficient to display Mn(++) induced nicking activity. ..
  2. Kadokawa J, Shimohigoshi R, Yamashita K, Yamamoto K. Synthesis of chitin and chitosan stereoisomers by thermostable α-glucan phosphorylase-catalyzed enzymatic polymerization of α-D-glucosamine 1-phosphate. Org Biomol Chem. 2015;13:4336-43 pubmed publisher
    ..of such non-natural aminopolysaccharides was performed by the thermostable α-glucan phosphorylase (from Aquifex aeolicus VF5)-catalyzed enzymatic polymerization of α-D-glucosamine 1-phosphate (GlcN-1-P), via successive α-..
  3. Baba R, Yamamoto K, Kadokawa J. Synthesis of α(1→4)-linked non-natural mannoglucans by α-glucan phosphorylase-catalyzed enzymatic copolymerization. Carbohydr Polym. 2016;151:1034-1039 pubmed publisher
    ..of quite weak specificity for the recognition of substrates by thermostable α-glucan phosphorylase (from Aquifex aeolicus VF5), in this study, we investigated the enzymatic copolymerization of Glc-1-P with its analogue monomer, α-..
  4. Klenk H, Meier T, Durovic P, Schwass V, Lottspeich F, Dennis P, et al. RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J Mol Evol. 1999;48:528-41 pubmed
    ..This raised doubts not only about whether the original Bacteria were indeed like the hyperthermophiles, but also concerning the value of single-gene phylogenies for hypotheses about the evolution of organisms...
  5. Xu X, Kona F, Wang J, Lu J, Stemmler T, Gatti D. The catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop. Biochemistry. 2005;44:12434-44 pubmed
  6. Duewel H, Sheflyan G, Woodard R. Functional and biochemical characterization of a recombinant 3-Deoxy-D-manno-octulosonic acid 8-phosphate synthase from the hyperthermophilic bacterium Aquifex aeolicus. Biochem Biophys Res Commun. 1999;263:346-51 pubmed
    ..5 h (90 degrees C), 8.1 h (80 degrees C), and 30.3 h (70 degrees C). KdsA appeared to follow Michaelis-Menton kinetics with K(A5-P)(m) = 8 - 74 microM, K(PEP)(m) = 43-28 microM, and k(cat) = 0.4-2.0 s(-1) between 60 and 90 degrees C. ..
  7. Shulami S, Yaniv O, Rabkin E, Shoham Y, Baasov T. Cloning, expression, and biochemical characterization of 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P) synthase from the hyperthermophilic bacterium Aquifex pyrophilus. Extremophiles. 2003;7:471-81 pubmed
    ..These results indicate that A. pyrophilus KDO8P synthase is a metal-dependent enzyme. A C11A mutant of KDO8P synthase from A. pyrophulis retained less than 1% of the wild-type activity and was shown to be incapable of metal binding. ..
  8. Purcarea C, Fernando R, Evans H, Evans D. The sole serine/threonine protein kinase and its cognate phosphatase from Aquifex aeolicus targets pyrimidine biosynthesis. Mol Cell Biochem. 2008;311:199-213 pubmed publisher
    ..The Thr/Ser kinase, its cognate phosphatase and a protein substrate may be elements of a simple signaling pathway, perhaps the most primitive example of this mode of regulation described thus far. ..
  9. Zhang X, Meining W, Fischer M, Bacher A, Ladenstein R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons. J Mol Biol. 2001;306:1099-114 pubmed
    ..The findings indicate the influence of the optimization of hydrophobic and ionic contacts in gaining thermostability. ..

More Information

Publications114 found, 100 shown here

  1. Evdokimov A, Phan J, Tropea J, Routzahn K, Peters H, Pokross M, et al. Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion. Nat Struct Biol. 2003;10:789-93 pubmed publisher
  2. Knowlton J, Bubunenko M, Andrykovitch M, Guo W, Routzahn K, Waugh D, et al. A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants. Biochemistry. 2003;42:2275-81 pubmed publisher
    ..The importance of the ball-and-socket junction for the function of NusG is supported by the functional analysis of site-directed mutants...
  3. Zhang X, Meining W, Cushman M, Haase I, Fischer M, Bacher A, et al. A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus. J Mol Biol. 2003;328:167-82 pubmed
    ..A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, inorganic phosphate elimination, formation of the Schiff base and cyclization is proposed. ..
  4. Oganesyan V, Busso D, Brandsen J, Chen S, Jancarik J, Kim R, et al. Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus. Acta Crystallogr D Biol Crystallogr. 2003;59:1219-23 pubmed
  5. Menichelli E, Edgcomb S, Recht M, Williamson J. The structure of Aquifex aeolicus ribosomal protein S8 reveals a unique subdomain that contributes to an extremely tight association with 16S rRNA. J Mol Biol. 2012;415:489-502 pubmed publisher
    ..These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA...
  6. Valle M, Sengupta J, Swami N, Grassucci R, Burkhardt N, Nierhaus K, et al. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 2002;21:3557-67 pubmed publisher
  7. Xu D, Liu G, Xiao R, Acton T, Goldsmith Fischman S, Honig B, et al. NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold. Proteins. 2004;54:794-6 pubmed
  8. Osawa T, Inanaga H, Numata T. Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:508-11 pubmed publisher
    ..6, b = 213.3, c = 231.7 A and a = 119.4, b = 98.0, c = 129.6 A, beta = 90.002 degrees , respectively. The asymmetric units of these crystals are expected to contain two and four molecules, respectively. ..
  9. Kanaujia S, Jeyakanthan J, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K. Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:2-16 pubmed publisher
    ..The results obtained are further compared with those obtained for homologous eukaryotic proteins. ..
  10. Herve G, Evans H, Fernado R, Patel C, Hachem F, Evans D. Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure. J Biol Chem. 2017;292:629-637 pubmed publisher
    ..The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues. ..
  11. Wang J, Duewel H, Woodard R, Gatti D. Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis. Biochemistry. 2001;40:15676-83 pubmed
    ..Overall, the process can be described as a syn addition of water and A5P to the si side of PEP. ..
  12. Blaszczyk J, Tropea J, Bubunenko M, Routzahn K, Waugh D, Court D, et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure. 2001;9:1225-36 pubmed
    ..The valley can accommodate a dsRNA substrate. Mn(2+) binding has significant impact on crystal packing, intermolecular interactions, thermal stability, and the formation of two RNA-cutting sites within each compound active center...
  13. Gan J, Shaw G, Tropea J, Waugh D, Court D, Ji X. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol. 2008;67:143-54 pubmed publisher
    ..Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction...
  14. Fukui K, Iino H, Baba S, Kumasaka T, Kuramitsu S, Yano T. Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus. Biochim Biophys Acta Proteins Proteom. 2017;1865:1178-1187 pubmed publisher
    ..On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule. ..
  15. Shin D, Yokota H, Kim R, Kim S. Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc Natl Acad Sci U S A. 2002;99:7980-5 pubmed
    ..There are several highly conserved residues in these putative active sites. The structure based molecular properties and thermostability of the protein are discussed. ..
  16. Steiner T, Kaiser J, Marinkovi S, Huber R, Wahl M. Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities. EMBO J. 2002;21:4641-53 pubmed
    ..The results strongly argue that both protein and nucleic acid contacts are important for NusG's functions and that the factor can act as an adaptor mediating indirect protein-nucleic acid associations...
  17. Korepanov A, Gongadze G, Garber M. General stress protein CTC from Bacillus subtilis specifically binds to ribosomal 5S RNA. Biochemistry (Mosc). 2004;69:607-11 pubmed
    ..The protein CTC from A. aeolicus, which is 50 amino acid residues shorter from the N-terminus than the proteins TL5 from T. thermophilus and CTC from B. subtilis, does not interact with 5S rRNA. ..
  18. Jeyakanthan J, Thamotharan S, Panjikar S, Kitamura Y, Nakagawa N, Shinkai A, et al. Expression, purification and X-ray analysis of 1,3-propanediol dehydrogenase (Aq_1145) from Aquifex aeolicus VF5. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:184-6 pubmed publisher
    ..SeMet-labelled 1,3-propanediol dehydrogenase protein from the hyperthermophilic bacterium Aquifex aeolicus VF5 was overexpressed in Escherichia coli and purified to homogeneity...
  19. Horita S, Yamanaka Y, Yamamura A, Okada A, Nakayama J, Nagata K, et al. Crystallization and preliminary X-ray analysis of a putative sensor histidine kinase domain: the C-terminal domain of HksP4 from Aquifex aeolicus VF5. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:803-7 pubmed publisher
    The histidine kinase domain of the cytoplasmic protein HksP4 from the hyperthermophilic bacterium Aquifex aeolicus VF5, located in the C-terminal half of the protein, was expressed, purified and crystallized...
  20. Yeh A, Ambroggio X, Andrade S, Einsle O, Chatelet C, Meyer J, et al. High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus. J Biol Chem. 2002;277:34499-507 pubmed
  21. Coggins B, McClerren A, Jiang L, Li X, Rudolph J, Hindsgaul O, et al. Refined solution structure of the LpxC-TU-514 complex and pKa analysis of an active site histidine: insights into the mechanism and inhibitor design. Biochemistry. 2005;44:1114-26 pubmed
    ..These results provide a structural basis for the design of more potent LpxC inhibitors than those that are currently available. ..
  22. Doucleff M, Malak L, Pelton J, Wemmer D. The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70. J Biol Chem. 2005;280:41530-6 pubmed publisher
    ..The homology of this structure with other DNA-binding proteins, combined with previous biochemical data, suggests how the C-terminal domain of sigma54 binds to DNA...
  23. Erzberger J, Pirruccello M, Berger J. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J. 2002;21:4763-73 pubmed
  24. Luke K, Apiyo D, Wittung Stafshede P. Role of the unique peptide tail in hyperthermostable Aquifex aeolicus cochaperonin protein 10. Biochemistry. 2005;44:14385-95 pubmed
    ..Taken together, the unique tail in Aacpn10 is not required for heptamer structure, stability, or function; instead, it appears to be an ancient strategy to avoid cochaperonin aggregation at extreme temperatures. ..
  25. Gennadios H, Christianson D. Binding of uridine 5'-diphosphate in the "basic patch" of the zinc deacetylase LpxC and implications for substrate binding. Biochemistry. 2006;45:15216-23 pubmed
    ..The structures of the LpxC-UDP and LpxC-pyrophosphate complexes provide new insights with regard to substrate recognition in the basic patch and metal ion coordination in the active site of LpxC. ..
  26. Antonyuk S, Strange R, Ellis M, Bessho Y, Kuramitsu S, Inoue Y, et al. Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:1209-13 pubmed publisher
    ..Each subunit of the homodimer was found to be in a ;closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft. ..
  27. Jeyakanthan J, Kanaujia S, Nishida Y, Nakagawa N, Praveen S, Shinkai A, et al. Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5. Acta Crystallogr D Biol Crystallogr. 2010;66:116-24 pubmed publisher
    ..In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule. ..
  28. Molloy R, Ma W, Allen A, Greenwood K, Bryan L, Sacora R, et al. Aquifex aeolicus FlgM protein exhibits a temperature-dependent disordered nature. Biochim Biophys Acta. 2010;1804:1457-66 pubmed publisher
    ..Based on our results, we propose that at 20 degrees C the A. aeolicus FlgM assumes a four-helix bundle-like conformation that becomes a more extended conformation at the A. aeolicus' physiological temperature of 85 degrees C. ..
  29. Keasling J, Bertsch L, Kornberg A. Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase. Proc Natl Acad Sci U S A. 1993;90:7029-33 pubmed
    ..13 mM); the kcat for the poly(P)ase activity is 1.1 s-1 and that for pppGpp hydrolase is 0.023 s-1. These and other findings direct attention to possible functions of poly(P) in the response of E. coli to stresses and deprivations...
  30. Morales A, Swairjo M, Schimmel P. Structure-specific tRNA-binding protein from the extreme thermophile Aquifex aeolicus. EMBO J. 1999;18:3475-83 pubmed
  31. Kona F, Xu X, Martin P, Kuzmic P, Gatti D. Structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-D-manno-octulosonate 8-phosphate synthases. Biochemistry. 2007;46:4532-44 pubmed publisher
    ..These differences may reflect an evolutionary adaptation of metallo and nonmetallo KDO8PS's to the cellular concentrations of these metabolites in their respective hosts...
  32. Xu X, Wang J, Grison C, Petek S, Coutrot P, Birck M, et al. Structure-based design of novel inhibitors of 3-deoxy-D-manno-octulosonate 8-phosphate synthase. Drug Des Discov. 2003;18:91-9 pubmed
    ..The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS. ..
  33. Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, et al. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J Biol Chem. 2005;280:16002-8 pubmed publisher
    ..This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop...
  34. Antonyuk S, Ellis M, Strange R, Bessho Y, Kuramitsu S, Shinkai A, et al. Structure of SurE protein from Aquifex aeolicus VF5 at 1.5 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:1204-8 pubmed publisher
    ..The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium. ..
  35. Alberdi E, Weldon J, Becerra S. Glycosaminoglycans in human retinoblastoma cells: heparan sulfate, a modulator of the pigment epithelium-derived factor-receptor interactions. BMC Biochem. 2003;4:1 pubmed
    ..These data indicate that retinoblastoma cells secrete heparin/heparan sulfate with binding affinity for PEDF, which may be important in efficient cell-surface receptor binding. ..
  36. 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...
  37. Buetow L, Dawson A, Hunter W. The nucleotide-binding site of Aquifex aeolicus LpxC. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:1082-6 pubmed
    ..However, based on the position of uracil revealed in this study and on the previously reported complex of LpxC with an inhibitor, a model is proposed for substrate binding. ..
  38. Tomikawa C, Hori H. The core domain of Aquifex aeolicus tRNA (m7G46) methyltransferase has the methyl-transfer activity to tRNA. Nucleic Acids Symp Ser (Oxf). 2006;:245-6 pubmed
    ..Thus, the core domain of the A. aeolicus TrmB has a methyl-transfer activity. ..
  39. Swairjo M, Otero F, Yang X, Lovato M, Skene R, McRee D, et al. Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Mol Cell. 2004;13:829-41 pubmed
    ..It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s...
  40. Shin H, Gennadios H, Whittington D, Christianson D. Amphipathic benzoic acid derivatives: synthesis and binding in the hydrophobic tunnel of the zinc deacetylase LpxC. Bioorg Med Chem. 2007;15:2617-23 pubmed
    ..We conclude that the intermolecular interactions in the hydrophobic tunnel dominate enzyme affinity in this series of benzoic acid derivatives. ..
  41. Itoh Y, Sekine S, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of Aquifex aeolicus SelA, a bacterial selenocysteine synthase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68:1128-33 pubmed publisher
    ..Truncation of the N-terminal region (?N) also improved the resolution. A 3.3 Å resolution data set for phase determination was obtained from a crystal of selenomethionine-substituted Lys-methylated SelA-?N. ..
  42. Reizer J, Reizer A, Saier M, Bork P, Sander C. Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily. Trends Biochem Sci. 1993;18:247-8 pubmed
  43. Bocchetta M, Ceccarelli E, Creti R, Sanangelantoni A, Tiboni O, Cammarano P. Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences. J Mol Evol. 1995;41:803-12 pubmed
  44. Lim J, Yu Y, Choi I, Ryu J, Ahn B, Kim S, et al. Cloning and expression of superoxide dismutase from Aquifex pyrophilus, a hyperthermophilic bacterium. FEBS Lett. 1997;406:142-6 pubmed
    ..The metal binding residues found in all SOD sequences from different species are also conserved in A. pyrophilus SOD. The protein is biochemically active only as an oligomer and is resistant to thermal denaturation...
  45. Uchiyama S, Nakano H, Kashimori H, Kijima H, Ohshima T, Saihara Y, et al. Solution structure of the ribosome recycling factor from Aquifex aeolicus. Biochemistry. 2001;40:2387-96 pubmed
    ..These results indicate that the joint region between two domains contributes to the fluctuation in the orientation of two domains. Thus, it was shown that RRF remains the tRNA mimicry in solution where it functions...
  46. Raibaud S, Lebars I, Guillier M, Chiaruttini C, Bontems F, Rak A, et al. NMR structure of bacterial ribosomal protein l20: implications for ribosome assembly and translational control. J Mol Biol. 2002;323:143-51 pubmed
    ..The pre-folded C-terminal domain would make a primary interaction with a specific site on the 23S rRNA. The N-terminal domain would then fold within the ribosome, participating in its correct 3D assembly...
  47. Ogle J, Murphy F, Tarry M, Ramakrishnan V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell. 2002;111:721-32 pubmed
    ..We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity...
  48. Ishii R, Nureki O, Yokoyama S. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. J Biol Chem. 2003;278:32397-404 pubmed publisher
    ..Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs...
  49. Doucleff M, Chen B, Maris A, Wemmer D, Kondrashkina E, Nixon B. Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria. J Mol Biol. 2005;353:242-55 pubmed publisher
    ..These analyses also raise the possibility that a structured linker between N-terminal regulatory and central output domains is used frequently in regulatory proteins from hyperthermophilic organisms...
  50. Gan J, Tropea J, Austin B, Court D, Waugh D, Ji X. Intermediate states of ribonuclease III in complex with double-stranded RNA. Structure. 2005;13:1435-42 pubmed publisher
    ..Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates...
  51. Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, et al. Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism. Biochemistry. 2007;46:9513-22 pubmed publisher
    ..On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed...
  52. Das R, Loss S, Li J, Waugh D, Tarasov S, Wingfield P, et al. Structural biophysics of the NusB:NusE antitermination complex. J Mol Biol. 2008;376:705-20 pubmed publisher
    ..There is one loop of residues (from 113 to 118 in NusB) affected by NusE binding in the ternary complex but not in the binary complex. This difference may be correlated to an increase in binding affinity of RNA for the NusB/NusE complex...
  53. Awai T, Ochi A, Ihsanawati -, Sengoku T, Hirata A, Bessho Y, et al. Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. J Biol Chem. 2011;286:35236-46 pubmed publisher
    ..Thus, this docking model introduces a rational explanation of the multisite specificity of A. aeolicus Trm1. ..
  54. Chatelet C, Gaillard J, P tillot Y, Louwagie M, Meyer J. A [2Fe-2S] protein from the hyperthermophilic bacterium Aquifex aeolicus. Biochem Biophys Res Commun. 1999;261:885-9 pubmed publisher
    ..The A. aeolicus [2Fe-2S] protein is thus representative of a presumably novel protein fold involved in a variety of functions in very diverse cellular backgrounds...
  55. Duewel H, Radaev S, Wang J, Woodard R, Gatti D. Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism. J Biol Chem. 2001;276:8393-402 pubmed publisher
    ..Abstraction of a proton from either of these water molecules by a protein group is expected to elicit a nucleophilic attack of the resulting hydroxide ion on the nearby C-2(PEP), thus triggering the beginning of the catalytic cycle...
  56. Meyer J, Clay M, Johnson M, Stubna A, M nck E, Higgins C, et al. A hyperthermophilic plant-type [2Fe-2S] ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond. Biochemistry. 2002;41:3096-108 pubmed
    ..This observation is consistent with the large distance (ca. 20 A) that is predicted to separate the iron-sulfur chromophore from the disulfide bridge...
  57. Sharples G, Bolt E, Lloyd R. RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions. Mol Microbiol. 2002;44:549-59 pubmed
    ..aeolicus RusA shows a different sequence preference (3' to TG) from the E. coli protein (5' to CC), and the r1t RusA has relaxed sequence dependence, requiring only a single cytosine...
  58. Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J. Visualizing tmRNA entry into a stalled ribosome. Science. 2003;300:127-30 pubmed publisher
    ..The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA...
  59. Whittington D, Rusche K, Shin H, Fierke C, Christianson D. Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis. Proc Natl Acad Sci U S A. 2003;100:8146-50 pubmed publisher
    ..Notably, simple inhibitors designed to target interactions in the hydrophobic tunnel bind with micromolar affinity, thereby representing a step toward the structure-based design of a potent, broad-spectrum antibacterial drug...
  60. Lee S, De La Torre A, Yan D, Kustu S, Nixon B, Wemmer D. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 2003;17:2552-63 pubmed publisher
    ..The extended, structured loops from the subunits of the heptamer localize to a pore in the center of the ring and form a surface that could contact sigma54...
  61. Kristensen O, Laurberg M, Liljas A, Kastrup J, Gajhede M. Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry. 2004;43:8894-900 pubmed publisher
    ..Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily...
  62. Khademi S, O Connell J, Remis J, Robles Colmenares Y, Miercke L, Stroud R. Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science. 2004;305:1587-94 pubmed publisher
    ..Favorable interactions for NH3 are seen within the channel and use conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB conducts uncharged NH3...
  63. Ahuja A, Purcarea C, Ebert R, Sadecki S, Guy H, Evans D. Aquifex aeolicus dihydroorotase: association with aspartate transcarbamoylase switches on catalytic activity. J Biol Chem. 2004;279:53136-44 pubmed publisher
    ..At pH 7.4, the equilibrium ratio of carbamoyl aspartate to dihydroorotate is 17 and complex formation may drive the reaction in the biosynthetic direction...
  64. Swairjo M, Schimmel P. Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc Natl Acad Sci U S A. 2005;102:988-93 pubmed publisher
    ..Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding...
  65. Martin P, Purcarea C, Zhang P, Vaishnav A, Sadecki S, GUY EVANS H, et al. The crystal structure of a novel, latent dihydroorotase from Aquifex aeolicus at 1.7A resolution. J Mol Biol. 2005;348:535-47 pubmed publisher
    ..coli dihydroorotase are located in disordered loops in both crystal structures of A.aeolicus dihydroorotase and may function as a disorder-to-order "entropy switch"...
  66. Yuan Y, Pei Y, Ma J, Kuryavyi V, Zhadina M, Meister G, et al. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell. 2005;19:405-19 pubmed publisher
    ..We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC...
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