Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Iyer, Larkshminarayan M ^a   Anantharaman, Vivek ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOTAXIS AFFECTING AGENT; GUANYLATE CYCLASE; HEME; HISTIDINE; LIGAND; METHYL GROUP; RECEPTOR; SIGNAL PEPTIDE; BACTERIAL PROTEIN; NITRIC OXIDE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ANIMAL GENETICS; ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; CONTROLLED STUDY; COVALENT BOND; GAS; GENE INTERACTION; GENETIC CODE; GENETIC CONSERVATION; HORIZONTAL GENE TRANSFER; NONHUMAN; OPERON; PHYLOGENY; PREDICTION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; ANIMAL; BINDING SITE; DIMERIZATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE;

ANIMALIA; BACTERIA (MICROORGANISMS);

ANIMALS; BACTERIAL PROTEINS; BINDING SITES; CONSERVED SEQUENCE; DIMERIZATION; GUANYLATE CYCLASE; HEME; NITRIC OXIDE;

EID: 9144261238     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-5     Document Type: Article

References (47)

1. Lodish H, Berk A, Zipursky SL and Matsudaira P Molecular Cell Biology New York, NY: W H Freeman & Co 1999,
2. Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P Molecular Biology of the Cell New York, NY: Garland Pub 2002,
3. Taylor BL, Zhulin IB and Johnson MS Aerotaxis and other energy-sensing behavior in bacteria. Annu Rev Microbiol 1999, 53:103-128
4. Anantharaman V, Koonin EV and Aravind L Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol 2001, 307: 271-1292
5. Morais Cabral JH, Lee A, Cohen SL, Chait BT, Li M and Mackinnon R Crystal structure and functional analysis of the HERG potassium channel N terminus: a eukaryotic PAS domain. Cell 1998, 95:649-655
6. Martinez SE, Wu AY, Glavas NA, Tang XB, Turley S, Hol WG and Beavo JA The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding. Proc Natl Acad Sci U S A 2002, 99:13260-13265
7. Ho YS, Burden LM and Hurley JH Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. Embo J 2000, 19:5288-5299
8. Perutz MF, Paoli M and Lesk AM Fix L, a haemoglobin that acts as an oxygen sensor: signalling mechanism and structural basis of its homology with PAS domains. Chem Biol 1999, 6: R291-297
9. Gong W, Hao B, Mansy SS, Gonzalez G, Gilles-Gonzalez MA and Chan MK Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci U S A 1998, 95: 15177-15182
10. Aravind L, Mazumder R, Vasudevan S and Koonin EV Trends in protein evolution inferred from sequence and structure analysis. Curr Opin Struct Biol 2002, 12: 392-399
11. Ponting CP and Aravind L PAS: a multifunctional domain family comes to light. Curr Biol 1997, 7: R674-677
12. Zhulin IB, Taylor BL and Dixon R PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem Sci 1997, 22: 331-333
13. Aravind L and Ponting CP The GAF domain: an evolutionary link between diverse phototransducing proteins. Trends Biochem Sci 1997, 22: 458-459
14. Anantharaman V and Aravind L Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors. Trends Biochem Sci 2000, 25: 535-537
15. Aravind L and Koonin EV Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 1999, 287: 1023-1040
16. Snyder SH and Bredt DS Nitric oxide as a neuronal messenger. Trends Pharmacol Sci 1991, 12: 125-128
17. Denninger JW and Marletta MA Guanylate cyclase and the NO/cGMP signaling pathway. Biochim Biophys Acta 1999, 1411: 334-350
18. Murad F Regulation of cytosolic guanylyl cyclase by nitric oxide: the NO-cyclic GMP signal transduction system. Adv Pharmacol 1994, 26: 19-33
19. Moncada S, Palmer RM and Higgs EA Nitric oxide: physiology, pathophysiology, and pharmacology. Pharmacol Rev 1991, 43: 109-142
20. Marletta MA Nitric oxide synthase: aspects concerning structure and catalysis. Cell 1994, 78: 927-930
21. Wedel B, Humbert P, Harteneck C, Foerster J, Malkewitz J, Bohme E, Schultz G and Koesling D Mutation of His-105 in the beta 1 subunit yields a nitric oxide-insensitive form of soluble guanylyl cyclase. Proc Natl Acad Sci U S A 1994, 91: 2592-2596
22. Gerzer R, Bohme E, Hofmann F and Schultz G Soluble guanylate cyclase purified from bovine lung contains heme and copper. FEBS Lett 1981, 132: 71-74
23. Stone JR and Marletta MA Soluble guanylate cyclase from bovine lung: activation with nitric oxide and carbon monoxide and spectral characterization of the ferrous and ferric states. Biochemistry 1994, 33: 5636-5640
24. Lawson DM, Stevenson CE, Andrew CR and Eady RR Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase. Embo J 2000, 19: 5661-5671
25. Becker EM, Alonso-Alija C, Apeler H, Gerzer R, Minuth T, Pleibeta U, Schmidt P, Schramm M, Schroder H, Schroeder W, Steinke W, Straub A and Stasch JP NO-independent regulatory site of direct sGC stimulators like YC-1 and BAY 41-2272. BMC Pharmacol 2001, 1: 13
26. Stasch JP, Becker EM, Alonso-Alija C, Apeler H, Dembowsky K, Feurer A, Gerzer R, Minuth T, Perzborn E, Pleiss U, Schroder H, Schroeder W, Stahl E, Steinke W, Straub A and Schramm M NO-independent regulatory site on soluble guanylate cyclase. Nature 2001, 410: 212-215
27. Wootton JC Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994, 18: 269-285
28. Foerster J, Harteneck C, Malkewitz J, Schultz G and Koesling D A functional heme-binding site of soluble guanylyl cyclase requires intact N-termini of alpha 1 and beta 1 subunits. Eur J Biochem 1996, 240: 380-386
29. Le Moual H and Koshland DE Jr Molecular evolution of the C-terminal cytoplasmic domain of a superfamily of bacterial receptors involved in taxis. J Mol Biol 1996, 261: 568-585
30. Aravind L and Ponting CP The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. FEMS Microbiol Lett 1999, 176: 111-116
31. Dandekar T, Snel B, Huynen M and Bork P Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 1998, 23: 324-328
32. Wolf YI, Rogozin IB, Kondrashov AS and Koonin EV Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 2001, 11: 356-372
33. Galperin MY, Natale DA, Aravind L and Koonin EV A specialized version of the HD hydrolase domain implicated in signal transduction. J Mol Microbiol Biotechnol 1999, 1: 303-305
34. Ausmees N, Mayer R, Weinhouse H, Volman G, Amikam D, Benziman M and Lindberg M Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity. FEMS Microbiol Lett 2001, 204: 163-167
35. Pei J and Grishin NV GGDEF domain is homologous to adenylyl cyclase. Proteins 2001, 42: 210-216
36. Anantharaman V and Aravind L The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem Sci 2001, 26: 579-582
37. Mougel C and Zhulin IB CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem Sci 2001, 26: 582-584
38. Adak S, Bilwes AM, Panda K, Hosfield D, Aulak KS, McDonald JF, Tainer JA, Getzoff ED, Crane BR and Stuehr DJ Cloning, expression, and characterization of a nitric oxide synthase protein from Deinococcus radiodurans. Proc Natl Acad Sci U S A 2002, 99: 107-112
39. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV and Daly MJ Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 2001, 65: 44-79
40. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389-3402
41. Notredame C, Higgins DG and Heringa J T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302: 205-217
42. Cuff JA, Clamp ME, Siddiqui AS, Finlay M and Barton GJ JPred: a consensus secondary structure prediction server. Bioinformatics 1998, 14: 892-893
43. Rost B and Sander C Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993, 232: 584-599
44. Rost B, Schneider R and Sander C Protein fold recognition by prediction-based threading. J Mol Biol 1997, 270: 471-480
45. Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L and Altschul SF IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999, 15: 1000-1011
46. Felsenstein J Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 1996, 266: 418-427
47. Adachi J and Hasegawa M MOLPHY: Programs for Molecular Phylogenetics. Tokyo: Institute of Statistical Mathematics 1992,