methanococcaceae

Summary

Summary: A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.

Top Publications

  1. Bergeron L, Shis D, Gomez L, Clark D. Small molecule inhibition of a Group II chaperonin: pinpointing a loop region within the equatorial domain as necessary for protein refolding. Arch Biochem Biophys. 2009;481:45-51 pubmed publisher
    ..These results implicate a specific equatorial region of Group II chaperonins in the refolding of proteins, and suggest its importance in conformational changes that accompany chaperone function...
  2. Grochowski L, Censky K, Xu H, White R. A new class of adenylate kinase in methanogens is related to uridylate kinase. Arch Microbiol. 2012;194:141-5 pubmed publisher
    ..Here, we report that the MJ0458 gene product is a second type of archaeal adenylate kinase, AdkB. This enzyme is different from the established archaeal-specific adenylate kinase in both sequence and predicted tertiary structure...
  3. Grochowski L, Xu H, White R. An iron(II) dependent formamide hydrolase catalyzes the second step in the archaeal biosynthetic pathway to riboflavin and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Biochemistry. 2009;48:4181-8 pubmed publisher
    ..The identification of this enzyme confirms the involvement of GTP cyclohydrolase III (ArfA) in archaeal riboflavin and Fo biosynthesis...
  4. Takai K, Inoue A, Horikoshi K. Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int J Syst Evol Microbiol. 2002;52:1089-95 pubmed
    ..The name Methanothermococcus okinawensis sp. nov is proposed, with the type strain IH1T (=JCM 11175T=DSM 14208T)...
  5. Bergeron L, Lee C, Tokatlian T, Höllrigl V, Clark D. Chaperone function in organic co-solvents: experimental characterization and modeling of a hyperthermophilic chaperone subunit from Methanocaldococcus jannaschii. Biochim Biophys Acta. 2008;1784:368-78 pubmed
    ..These models suggest that thermodynamic stability and the reversibility of enzyme unfolding play key roles in the effectiveness of enzyme recovery by rTHS...
  6. Sakamoto K, Murayama K, Oki K, Iraha F, Kato Murayama M, Takahashi M, et al. Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Structure. 2009;17:335-44 pubmed publisher
    ..2 Angstroms resolutions by SAD phasing at CuK alpha and CrK alpha wavelengths, respectively. The native structure, determined by molecular replacement, revealed no significant structural distortion caused by iodotyrosine incorporation...
  7. Siggaard J, Johansson E, Vognsen T, Helt S, Harris P, Larsen S, et al. Concerted bifunctionality of the dCTP deaminase-dUTPase from Methanocaldococcus jannaschii: a structural and pre-steady state kinetic analysis. Arch Biochem Biophys. 2009;490:42-9 pubmed publisher
    ..A pre-steady state kinetic analysis of the bifunctional reaction and the dUTPase half-reaction supported a conformational change upon substrate binding in both reactions and a concerted catalytic step for the bifunctional reaction...
  8. Pritchett M, Wilkinson S, Geiduschek E, Ouhammouch M. Hybrid Ptr2-like activators of archaeal transcription. Mol Microbiol. 2009;74:582-93 pubmed publisher
    ..In contrast, the effector domain of Ptr1, the M. jannaschii Ptr2 paralogue, yields only very weak activation...
  9. Xia Z, He Y, Dai W, White S, Boyd G, Mathews F. Detailed active site configuration of a new crystal form of methanol dehydrogenase from Methylophilus W3A1 at 1.9 A resolution. Biochemistry. 1999;38:1214-20 pubmed
    ..The proximity of the hydroxyl of methanol to C5 of PQQ compared to the greater separation of the substrate methyl group from C5 supports the addition-elimination reaction mechanism involving a hemiketal intermediate...

More Information

Publications59

  1. Musiani F, Ippoliti E, Micheletti C, Carloni P, Ciurli S. Conformational fluctuations of UreG, an intrinsically disordered enzyme. Biochemistry. 2013;52:2949-54 pubmed publisher
    ..On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallochaperones necessary for the formation of multiprotein complexes known to be involved in urease activation...
  2. Zhou H, Liu Q, Gao Y, Teng M, Niu L. Crystal structure of NusG N-terminal (NGN) domain from Methanocaldococcus jannaschii and its interaction with rpoE''. Proteins. 2009;76:787-93 pubmed publisher
    ..MjNGN alone was found to be sufficient for rpoE'' binding and an MjNGN-rpoE'' model has been constructed by rigid docking...
  3. Kuan S, Chen H, Huang C, Chang C, Chen S, Yang C, et al. Crystallization and preliminary X-ray diffraction analysis of the Nif3-family protein MJ0927 from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:80-2 pubmed publisher
    ..47?Å and belonged to the orthorhombic space group C222, with unit-cell parameters a = 81.21, b = 172.94, c = 147.42?Å. Determination of this structure may provide insights into the function of MJ0927...
  4. Ruan B, Nakano H, Tanaka M, Mills J, DeVito J, Min B, et al. Cysteinyl-tRNA(Cys) formation in Methanocaldococcus jannaschii: the mechanism is still unknown. J Bacteriol. 2004;186:8-14 pubmed
    ..These results imply that it is not established that proS or MJ1477 gene products catalyze Cys-tRNA(Cys) synthesis in M. jannaschii. Thus, the mechanism of Cys-tRNA(Cys) formation in M. jannaschii still remains to be discovered...
  5. Newmister S, Otte M, Escalante Semerena J, Rayment I. Structure and mutational analysis of the archaeal GTP:AdoCbi-P guanylyltransferase (CobY) from Methanocaldococcus jannaschii: insights into GTP binding and dimerization. Biochemistry. 2011;50:5301-13 pubmed publisher
  6. Leigh J. Growth of methanogens under defined hydrogen conditions. Methods Enzymol. 2011;494:111-8 pubmed publisher
    ..Cultures whose growth is limited by hydrogen can be compared to cultures whose growth is limited by some other nutrient and are therefore under hydrogen excess...
  7. Martinez Cruz L, Encinar J, Sevilla P, Oyenarte I, Gómez García I, Aguado Llera D, et al. Nucleotide-induced conformational transitions in the CBS domain protein MJ0729 of Methanocaldococcus jannaschii. Protein Eng Des Sel. 2011;24:161-9 pubmed publisher
    ..Taken together, these results suggest that: (i) the adenosyl ligands bind to MJ0729 in different ways, and (ii) there are changes in the protein secondary structure upon binding of the nucleotides...
  8. Mehrotra S, Balaram H. Methanocaldococcus jannaschii adenylosuccinate synthetase: studies on temperature dependence of catalytic activity and structural stability. Biochim Biophys Acta. 2008;1784:2019-28 pubmed publisher
    ..The unfolding profiles could be described as a composite of atleast two distinct transitions, with a stable intermediate in the unfolding pathway...
  9. Clote P, Kranakis E, Krizanc D, Salvy B. Asymptotics of canonical and saturated RNA secondary structures. J Bioinform Comput Biol. 2009;7:869-93 pubmed
    ..We introduce a stochastic greedy method to sample random saturated structures, called quasi-random saturated structures, and show that the expected number of base pairs is 0.340633 . n. ..
  10. Gómez García I, Oyenarte I, Martinez Cruz L. The crystal structure of protein MJ1225 from Methanocaldococcus jannaschii shows strong conservation of key structural features seen in the eukaryal gamma-AMPK. J Mol Biol. 2010;399:53-70 pubmed publisher
  11. Basran J, Sutcliffe M, Scrutton N. Enzymatic H-transfer requires vibration-driven extreme tunneling. Biochemistry. 1999;38:3218-22 pubmed
    ..The results demonstrate that classical transition state theory and its tunneling derivatives do not adequately describe this enzymatic reaction...
  12. McGill T, Jurka J, Sobieski J, Pickett M, Woese C, Fox G. Characteristic archaebacterial 16S rRNA oligonucleotides. Syst Appl Microbiol. 1986;7:194-7 pubmed
    ..In the case of the Methanobacteriaceae the clustering methods suggest a specific relationship to the Methanococcaceae. This inclusion is in fact supported by six strong signature oligonucleotides...
  13. Helgadóttir S, Sinapah S, Soll D, Ling J. Mutational analysis of Sep-tRNA:Cys-tRNA synthase reveals critical residues for tRNA-dependent cysteine formation. FEBS Lett. 2012;586:60-3 pubmed publisher
    ..Our work thus represents the first systematic functional analysis of conserved residues in archaeal SepCysSs, providing insights into the catalytic and substrate binding mechanisms of this poorly characterized enzyme...
  14. Heindl H, Greenwell P, Weingarten N, Kiss T, Terstyanszky G, Weinzierl R. Cation-? interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain. Biochem Soc Trans. 2011;39:31-5 pubmed publisher
  15. Sheikh S, O Handley S, Dunn C, Bessman M. Identification and characterization of the Nudix hydrolase from the Archaeon, Methanococcus jannaschii, as a highly specific ADP-ribose pyrophosphatase. J Biol Chem. 1998;273:20924-8 pubmed
    ..This is the first Nudix hydrolase identified from the Archaea, indicating that the family of enzymes containing the Nudix signature sequence is represented in all three kingdoms...
  16. Zhang C, Liu C, Slater S, Hou Y. Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys). Nat Struct Mol Biol. 2008;15:507-14 pubmed publisher
    ..These results highlight the importance of the protein binary complex for efficient synthesis of Cys-tRNA(Cys)...
  17. Lipman R, Chen J, Evilia C, Vitseva O, Hou Y. Association of an aminoacyl-tRNA synthetase with a putative metabolic protein in archaea. Biochemistry. 2003;42:7487-96 pubmed
    ..The association of Mj1338 with ProRS, and with other components of the protein synthesis machinery, thus suggests the possibility of a closer link between metabolism and decoding in archaea than in eukarya or bacteria...
  18. Heyer J, Galchenko V, Dunfield P. Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology. 2002;148:2831-46 pubmed
    ..Soluble methane monooxygenase could not be detected in many Methylocystis strains either by an enzyme activity test (oxidation of naphthalene) or by PCR-based amplification of an mmoX gene...
  19. Ambrogelly A, Ahel I, Polycarpo C, Bunjun Srihari S, Krett B, Jacquin Becker C, et al. Methanocaldococcus jannaschii prolyl-tRNA synthetase charges tRNA(Pro) with cysteine. J Biol Chem. 2002;277:34749-54 pubmed publisher
    ..We discuss the implications of these results on the in vivo activity of the M. jannaschii ProRS and on the nature of the enzyme involved in the synthesis of Cys-tRNA(Cys) in M. jannaschii...
  20. McAllister S, Kral T. Methane production by methanogens following an aerobic washing procedure: simplifying methods for manipulation. Astrobiology. 2006;6:819-23 pubmed
    ..With the discovery of methane in the martian atmosphere, it is likely that there will be an increase in astrobiology-related methanogen research. The research reported here should simplify the methodology...
  21. Rangarajan S, Jeyakanthan J, Mridula P, Sakamoto K, Kitamura Y, Agari Y, et al. Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008;64:102-4 pubmed publisher
    ..1, b = 46.1, c = 98.5 A, and diffracted to a resolution of 1.9 A. Preliminary calculations reveal that the asymmetric unit contains two monomers with a Matthews coefficient (V(M)) of 2.16 A(3) Da(-1)...
  22. Clementino M, Vieira R, Cardoso A, Nascimento A, Silveira C, Riva T, et al. Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world. Extremophiles. 2008;12:595-604 pubmed publisher
    ..This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters...
  23. Balakrishna A, Manimekalai M, Hunke C, Gayen S, Rössle M, Jeyakanthan J, et al. Crystal and solution structure of the C-terminal part of the Methanocaldococcus jannaschii A1AO ATP synthase subunit E revealed by X-ray diffraction and small-angle X-ray scattering. J Bioenerg Biomembr. 2010;42:311-20 pubmed publisher
    ..jannaschii was determined using small angle X-ray scattering. Rigid body modeling of two copies of one of the monomer established a fit with a tail to tail arrangement...
  24. Ali R, Kumar S, Balaram H, Sarma S. 1H, 13C, 15N assignment and secondary structure determination of glutamine amido transferase subunit of gaunosine monophosphate synthetase from Methanocaldococcus jannaschii. Biomol NMR Assign. 2012;6:193-6 pubmed publisher
  25. Han B, Su T, Yang C, Jiang H, Wu H, Zhang C, et al. [Heterologous expression of particulate methane monooxygenase in different host cells]. Sheng Wu Gong Cheng Xue Bao. 2009;25:1151-9 pubmed
    ..In conclusion, correct fold of pMMO in the host cells is important for its functional expression...
  26. Lycklama A Nijeholt J, de Keyzer J, Prabudiansyah I, Driessen A. Characterization of the supporting role of SecE in protein translocation. FEBS Lett. 2013;587:3083-8 pubmed publisher
    ..This suggests that the SecY and SecE interactions are static, while the hinge region provides flexibility to allow the SecY pore to open. ..
  27. Graupner M, Xu H, White R. Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea. J Bacteriol. 2000;182:3688-92 pubmed
    ..We conclude that the MJ1425-encoded enzyme is likely to be involved in the biosynthesis of both coenzyme M and methanopterin...
  28. Oza J, Sowers K, Perona J. Linking energy production and protein synthesis in hydrogenotrophic methanogens. Biochemistry. 2012;51:2378-89 pubmed publisher
    ..These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions...
  29. Grochowski L, Xu H, White R. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J Bacteriol. 2006;188:3192-8 pubmed
    ..Unlike other known kinases associated with isoprene biosynthesis, Methanocaldococcus jannaschii isopentenyl phosphate kinase is predicted to be a member of the aspartokinase superfamily...
  30. Zhang Y, White R, Ealick S. Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry. 2008;47:205-17 pubmed publisher
    ..With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP...
  31. Kuratani M, Hirano M, Goto Ito S, Itoh Y, Hikida Y, Nishimoto M, et al. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. J Mol Biol. 2010;401:323-33 pubmed publisher
    ..We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4...
  32. Hoshino T, Nango E, Baba S, Eguchi T, Kumasaka T. Crystallization and preliminary X-ray analysis of isopentenyl diphosphate isomerase from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:101-3 pubmed publisher
    ..46, c=120.03?Å. The presence of one monomer per asymmetric unit gives a crystal volume per protein weight (VM) of 3.0?Å3?Da(-1) and a solvent constant of 59.0% by volume...
  33. Huang K, Ma J, Yuan Y, Gao Y. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of NifH2 from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:133-5 pubmed publisher
    ..85?Å. The crystals belonged to space group P2, with unit-cell parameters a=64.01, b=94.38, c=98.08?Å, ?=?=90, ?=98.85°...
  34. McDonald I, Uchiyama H, Kambe S, Yagi O, Murrell J. The soluble methane monooxygenase gene cluster of the trichloroethylene-degrading methanotroph Methylocystis sp. strain M. Appl Environ Microbiol. 1997;63:1898-904 pubmed
    ..strain M firmly in the genus Methylocystis. This is the first report of isolation and characterization of methane oxidation genes from methanotrophs of the genus Methylocystis...
  35. Sittka A, Sharma C, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol. 2009;6:266-75 pubmed
    ..It also suggests that the expression of heterologous RNA-binding proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo...
  36. Gagnon K, Zhang X, Maxwell E. In vitro reconstitution and affinity purification of catalytically active archaeal box C/D sRNP complexes. Methods Enzymol. 2007;425:263-82 pubmed
    ..This affinity selection protocol can provide highly purified complex in sufficient quantities not only for biochemical analyses but also for biophysical approaches such as cryoelectron microscopy and X-ray crystallography...
  37. Gómez García I, Kortazar D, Oyenarte I, Mato J, Martinez Chantar M, Martinez Cruz L. Purification, crystallization and preliminary crystallographic analysis of protein MJ1225 from Methanocaldococcus jannaschii, a putative archaeal homologue of gamma-AMPK. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:813-7 pubmed publisher
    ..95, c = 148.08 A, alpha = beta = 90.00, gamma = 120.00 degrees . Preliminary analysis of the X-ray data indicated that there was one molecule per asymmetric unit...
  38. Johansson E, Bjornberg O, Nyman P, Larsen S. Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases. J Biol Chem. 2003;278:27916-22 pubmed publisher
    ..The active site contains two water molecules that are engaged in hydrogen bonds to the invariant residues Ser118, Arg122, Thr130, and Glu145. These water molecules are potential nucleophile candidates in the deamination reaction...
  39. Tocchini Valentini G, Tocchini Valentini G. Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes. Proc Natl Acad Sci U S A. 2012;109:21325-9 pubmed publisher
  40. Ownby K, Xu H, White R. A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase. A new enzyme in purine biosynthesis. J Biol Chem. 2005;280:10881-7 pubmed publisher
    ..jannaschii cell extracts were incubated with H13CO3- and hydrogen gas. The presence of this signature gene in all of the Archaea indicates the presence of a purine biosynthetic pathway proceeding in the absence of folate coenzymes...
  41. Tanaka M, Yamada T, Itoh M, Okuda S, Goto S, Kanehisa M. Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Inform. 2006;17:230-9 pubmed
    ..As a result, we estimated enzymatic reaction contents of 227 common ancestors from 228 extant species, and found that links of several specific metabolites have frequently changed during the course of evolution...
  42. Christian T, Hou Y. Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases. J Mol Biol. 2007;373:623-32 pubmed
    ..Our results also shed new light onto the significance of the m1G37 modification in the controversial quadruplet-pairing model of tRNA frameshift suppressors...
  43. Grochowski L, White R. Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Ann N Y Acad Sci. 2008;1125:190-214 pubmed
    ..Some of the unique and uncanonical metabolic pathways that have been identified in the archaea with emphasis on the biochemistry of an obligate anaerobic methanogen, Methanocaldococcus jannaschii are reviewed...
  44. Lin Y, Lin L, Sriratana P, Coleman K, Ha T, Spies M, et al. Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds. J Bacteriol. 2008;190:5766-80 pubmed publisher
    ..On the basis of these results, different models that attempt to explain how intramolecular and intermolecular homologous recombination can generate novel forms of SSB or RPAs are proposed...
  45. Gayen S, Balakrishna A, Biukovic G, Yulei W, Hunke C, Gruber G. Identification of critical residues of subunit H in its interaction with subunit E of the A-ATP synthase from Methanocaldococcus jannaschii. FEBS J. 2008;275:1803-12 pubmed publisher
    ..The data presented provide, for the first time, structural insights into the interaction of subunits E and H, and their arrangement within A(1)A(0) ATP synthase...
  46. Grochowski L, Xu H, Leung K, White R. Characterization of an Fe(2+)-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii. Biochemistry. 2007;46:6658-67 pubmed
    ..MptA was found to require Fe2+ for activity. Mutation of conserved histidine residues H200N, H293N, and H295N, expected to be involved in Fe2+ binding, resulted in reduced enzymatic activity but no reduction in the amount of bound iron...
  47. Boonyaratanakornkit B, Miao L, Clark D. Transcriptional responses of the deep-sea hyperthermophile Methanocaldococcus jannaschii under shifting extremes of temperature and pressure. Extremophiles. 2007;11:495-503 pubmed
    ..jannaschii, the core pressure response was remarkably limited and consisted of differential expression of genes encoding three hypothetical proteins and a gene involved in DNA recombination...
  48. Weinzierl R. Nanomechanical constraints acting on the catalytic site of cellular RNA polymerases. Biochem Soc Trans. 2010;38:428-32 pubmed publisher
    ..In addition, many mutations within this domain cause a substantial increase in the RNAP catalytic activity ('superactivity'), suggesting that the RNAP active site is conformationally constrained...
  49. Chang S, Wallar B, Lipscomb J, Mayo K. Solution structure of component B from methane monooxygenase derived through heteronuclear NMR and molecular modeling. Biochemistry. 1999;38:5799-812 pubmed
    ..This NMR-derived structure of MMOB, therefore, presents the first high-resolution structure of a small protein effector of a nonheme oxygenase system...
  50. Elango N, Radhakrishnan R, Froland W, Wallar B, Earhart C, Lipscomb J, et al. Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci. 1997;6:556-68 pubmed
    ..Fifteen additional sequence differences distributed randomly over the three chains were also observed, including D alpha 209E, a ligand of one of the irons...