title: Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10.
abstract: Pseudouridines (Ψ) are found in structurally and functionally important regions of RNAs. Six families of Ψ synthases, TruA, TruB, TruD, RsuA, RluA, and Pus10 have been identified. Pus10 is present in Archaea and Eukarya. While most archaeal Pus10 produce both tRNA Ψ54 and Ψ55, some produce only Ψ55. Interestingly, human PUS10 has been implicated in apoptosis and Crohn's and Celiac diseases. Homology models of archaeal Pus10 proteins based on the crystal structure of human PUS10 reveal that there are subtle structural differences in all of these Pus10 proteins. These observations suggest that structural changes in homologous proteins may lead to loss, gain, or change of their functions, warranting the need to study the structure-function relationship of these proteins. Using comparison of structural models and a series of mutations, we identified forefinger loop (reminiscent of that of RluA) and an Arg and a Tyr residue of archaeal Pus10 as critical determinants for its Ψ54, but not for its Ψ55 activity. We also found that a Leu residue, in addition to the catalytic Asp, is essential for both activities. Since forefinger loop is needed for both rRNA and tRNA Ψ synthase activities of RluA, but only for tRNA Ψ54 activity of Pus10, archaeal Pus10 proteins must use a different mechanism of recognition for Ψ55 activity. We propose that archaeal Pus10 uses two distinct mechanisms for substrate uridine recognition and binding. However, since we did not observe any mutation that affected only Ψ55 activity, both mechanisms for archaeal Pus10 activities must share some common features.
authors.affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA.
authors.forename: Archi
authors.initials: A
authors.lastname: Joardar
authors.forename: Sujata
authors.initials: S
authors.lastname: Jana
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Fitzek
authors.forename: Priyatansh
authors.initials: P
authors.lastname: Gurha
authors.forename: Mrinmoyee
authors.initials: M
authors.lastname: Majumder
authors.forename: Kunal
authors.initials: K
authors.lastname: Chatterjee
authors.forename: Matt
authors.initials: M
authors.lastname: Geisler
authors.forename: Ramesh
authors.initials: R
authors.lastname: Gupta
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000235:genetics* / Q000378:metabolism*; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020029:Base Pairing; D019751:Intramolecular Transferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011560:Pseudouridine / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D012335:RNA, Ribosomal; D011560:Pseudouridine; D012343:RNA, Transfer; D019751:Intramolecular Transferases; C096995:pseudouridine synthases
keywords: Methanocaldococcus; Pseudouridine synthase; Pyrococcus; RNA modification; RluA; TruB
references.citation: IUBMB Life. 2000 May;49(5):341-51
references.pmid: 10902565
references.citation: Chromosoma. 2005 May;114(1):1-14
references.pmid: 15770508
references.citation: Sci Rep. 2012;2:663
references.pmid: 22993689
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D159-62
references.pmid: 18957446
references.citation: Nucleic Acids Res. 2000 Jun 15;28(12):2342-52
references.pmid: 10871366
references.citation: RNA. 2000 Jun;6(6):844-60
references.pmid: 10864043
references.citation: Nucleic Acids Res. 2005 Jul 18;33(13):3955-64
references.pmid: 16027442
references.citation: Nucleic Acids Res. 1995 Dec 25;23(24):5020-6
references.pmid: 8559660
references.citation: Cold Spring Harb Symp Quant Biol. 2001;66:147-59
references.pmid: 12762017
references.citation: RNA Biol. 2010 Mar-Apr;7(2):192-204
references.pmid: 20215871
references.citation: Chem Biol. 2006 Nov;13(11):1125-35
references.pmid: 17113994
references.citation: J Biol Chem. 2004 Jun 4;279(23):24585-91
references.pmid: 15028724
references.citation: Nucleic Acids Res. 2008 May;36(8):2459-75
references.pmid: 18304947
references.citation: Curr Opin Chem Biol. 2001 Jun;5(3):302-7
references.pmid: 11479122
references.citation: Nucleic Acids Res. 2006;34(15):4293-301
references.pmid: 16920741
references.citation: Curr Opin Microbiol. 2005 Dec;8(6):685-94
references.pmid: 16256421
references.citation: J Biol Chem. 2002 Aug 23;277(34):30445-53
references.pmid: 12058040
references.citation: Mol Cell. 2006 Nov 17;24(4):535-45
references.pmid: 17188032
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Methods Enzymol. 2007;425:21-53
references.pmid: 17673078
references.citation: Cell. 1982 Mar;28(3):543-50
references.pmid: 7074684
references.citation: RNA. 2012 Mar;18(3):421-33
references.pmid: 22274953
references.citation: Nucleic Acids Res. 2004 Feb 27;32(4):1422-9
references.pmid: 14990747
references.citation: RNA. 2008 Dec;14(12):2521-7
references.pmid: 18952823
references.citation: Trends Biochem Sci. 2002 Jul;27(7):344-51
references.pmid: 12114023
references.citation: Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760-4
references.pmid: 377283
references.citation: Nucleic Acids Res. 2007;35(16):5610-24
references.pmid: 17704128
references.citation: J Bacteriol. 1991 May;173(10):3138-48
references.pmid: 1708763
references.citation: Mol Cell. 2003 Sep;12(3):627-37
references.pmid: 14527409
references.citation: J Biol Chem. 1980 May 25;255(10):4387-90
references.pmid: 6768721
references.citation: Electrophoresis. 2009 Jun;30 Suppl 1:S162-73
references.pmid: 19517507
references.citation: Nucleic Acids Res. 1997 Nov 15;25(22):4493-9
references.pmid: 9358157
references.citation: Biochemistry. 1994 Jun 28;33(25):7869-76
references.pmid: 7516708
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12648-53
references.pmid: 14566049
references.citation: Cell. 2002 Apr 19;109(2):145-8
references.pmid: 12007400
references.citation: PLoS Genet. 2011 Jan 27;7(1):e1001283
references.pmid: 21298027
references.citation: J Mol Biol. 1970 Jul 14;51(1):83-100
references.pmid: 4921251
references.citation: Wiley Interdiscip Rev RNA. 2012 May-Jun;3(3):397-414
references.pmid: 22065625
references.citation: Mol Microbiol. 2008 Jan;67(2):323-35
references.pmid: 18069966
references.citation: J Biol Chem. 1980 Sep 10;255(17):8296-302
references.pmid: 6997293
references.citation: Curr Opin Struct Biol. 2004 Jun;14(3):335-43
references.pmid: 15193314
references.citation: RNA. 2008 Sep;14(9):1895-906
references.pmid: 18648068
references.citation: RNA. 2003 Jun;9(6):711-21
references.pmid: 12756329
references.citation: Nucleic Acids Res. 2009 Dec;37(22):7665-77
references.pmid: 19820108
references.citation: J Bacteriol. 2002 Oct;184(19):5348-57
references.pmid: 12218021
references.citation: RNA. 1995 Mar;1(1):102-12
references.pmid: 7489483
references.citation: Science. 1989 Jun 2;244(4908):1081-5
references.pmid: 2471267
references.citation: J Biol Chem. 1986 Jul 25;261(21):9703-9
references.pmid: 2426253
references.citation: Nat Protoc. 2009;4(1):1-13
references.pmid: 19131951
references.citation: Proteins. 2004 Jul 1;56(1):143-56
references.pmid: 15162494
references.citation: J Bacteriol. 1980 May;142(2):371-9
references.pmid: 6247318
references.citation: RNA Biol. 2007 Oct;4(2):101-9
references.pmid: 17993784
references.citation: J Mol Biol. 2007 Nov 9;373(5):1243-54
references.pmid: 17900615
references.citation: Bioinformatics. 2002 Aug;18(8):1141-2
references.pmid: 12176841
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D195-201
references.pmid: 21071406
references.citation: Gene. 1988 Sep 30;69(2):301-15
references.pmid: 3069586
references.citation: EMBO J. 2011 Jan 5;30(1):79-89
references.pmid: 21131909
references.citation: Trends Biochem Sci. 2013 Apr;38(4):210-8
references.pmid: 23391857
references.citation: J Biol Chem. 2003 Jan 10;278(2):695-8
references.pmid: 12431975
references.citation: Protein Sci. 2005 Aug;14(8):2201-6
references.pmid: 15987897
references.citation: Cell. 2001 Dec 28;107(7):929-39
references.pmid: 11779468
references.citation: J Biol Chem. 1984 Aug 10;259(15):9461-71
references.pmid: 6746655
references.citation: RNA. 2011 Jul;17(7):1367-80
references.pmid: 21628430
references.citation: J Biol Chem. 2010 Jan 8;285(2):805-9
references.pmid: 19917616
references.citation: Biochemistry. 2005 Nov 29;44(47):15488-94
references.pmid: 16300397