RRP41_SACS2
ID RRP41_SACS2 Reviewed; 248 AA.
AC Q9UXC2;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 114.
DE RecName: Full=Exosome complex component Rrp41 {ECO:0000255|HAMAP-Rule:MF_00591};
DE EC=3.1.13.- {ECO:0000255|HAMAP-Rule:MF_00591};
GN Name=rrp41 {ECO:0000255|HAMAP-Rule:MF_00591}; OrderedLocusNames=SSO0735;
OS Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
OS (Sulfolobus solfataricus).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Saccharolobus.
OX NCBI_TaxID=273057;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=10701121; DOI=10.1139/g99-108;
RA Charlebois R.L., Singh R.K., Chan-Weiher C.C.-Y., Allard G., Chow C.,
RA Confalonieri F., Curtis B., Duguet M., Erauso G., Faguy D., Gaasterland T.,
RA Garrett R.A., Gordon P., Jeffries A.C., Kozera C., Kushwaha N., Lafleur E.,
RA Medina N., Peng X., Penny S.L., She Q., St Jean A., van der Oost J.,
RA Young F., Zivanovic Y., Doolittle W.F., Ragan M.A., Sensen C.W.;
RT "Gene content and organization of a 281-kbp contig from the genome of the
RT extremely thermophilic archaeon, Sulfolobus solfataricus P2.";
RL Genome 43:116-136(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=11427726; DOI=10.1073/pnas.141222098;
RA She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J.,
RA Chan-Weiher C.C.-Y., Clausen I.G., Curtis B.A., De Moors A., Erauso G.,
RA Fletcher C., Gordon P.M.K., Heikamp-de Jong I., Jeffries A.C., Kozera C.J.,
RA Medina N., Peng X., Thi-Ngoc H.P., Redder P., Schenk M.E., Theriault C.,
RA Tolstrup N., Charlebois R.L., Doolittle W.F., Duguet M., Gaasterland T.,
RA Garrett R.A., Ragan M.A., Sensen C.W., Van der Oost J.;
RT "The complete genome of the crenarchaeon Sulfolobus solfataricus P2.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:7835-7840(2001).
RN [3]
RP INTERACTION WITH EXOSOME.
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=12947419; DOI=10.1038/sj.embor.embor929;
RA Evguenieva-Hackenberg E., Walter P., Hochleitner E., Lottspeich F.,
RA Klug G.;
RT "An exosome-like complex in Sulfolobus solfataricus.";
RL EMBO Rep. 4:889-893(2003).
RN [4]
RP INTERACTION WITH EXOSOME.
RX PubMed=17078816; DOI=10.1111/j.1365-2958.2006.05393.x;
RA Walter P., Klein F., Lorentzen E., Ilchmann A., Klug G.,
RA Evguenieva-Hackenberg E.;
RT "Characterization of native and reconstituted exosome complexes from the
RT hyperthermophilic archaeon Sulfolobus solfataricus.";
RL Mol. Microbiol. 62:1076-1089(2006).
RN [5]
RP FUNCTION, AND SUBUNIT.
RX PubMed=20488184; DOI=10.1016/j.febslet.2010.05.014;
RA Roppelt V., Klug G., Evguenieva-Hackenberg E.;
RT "The evolutionarily conserved subunits Rrp4 and Csl4 confer different
RT substrate specificities to the archaeal exosome.";
RL FEBS Lett. 584:2931-2936(2010).
RN [6]
RP INTERACTION WITH EXOSOME.
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=22503705; DOI=10.1016/j.biochi.2012.03.026;
RA Witharana C., Roppelt V., Lochnit G., Klug G., Evguenieva-Hackenberg E.;
RT "Heterogeneous complexes of the RNA exosome in Sulfolobus solfataricus.";
RL Biochimie 94:1578-1587(2012).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP42, SUBUNIT, AND
RP MUTAGENESIS OF ARG-98 AND ARG-99.
RX PubMed=16285928; DOI=10.1016/j.molcel.2005.10.020;
RA Lorentzen E., Conti E.;
RT "Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage
RT by an exosome RNase PH core.";
RL Mol. Cell 20:473-481(2005).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP42, FUNCTION,
RP SUBUNIT, AND MUTAGENESIS OF ASP-182.
RX PubMed=15951817; DOI=10.1038/nsmb952;
RA Lorentzen E., Walter P., Fribourg S., Evguenieva-Hackenberg E., Klug G.,
RA Conti E.;
RT "The archaeal exosome core is a hexameric ring structure with three
RT catalytic subunits.";
RL Nat. Struct. Mol. Biol. 12:575-581(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP42 AND RRP4,
RP FUNCTION, RNA-BINDING, AND SUBUNIT.
RX PubMed=17380186; DOI=10.1038/sj.embor.7400945;
RA Lorentzen E., Dziembowski A., Lindner D., Seraphin B., Conti E.;
RT "RNA channelling by the archaeal exosome.";
RL EMBO Rep. 8:470-476(2007).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) OF 4-248 IN COMPLEX WITH RRP42 AND
RP RRP4.
RX PubMed=20090900; DOI=10.1371/journal.pone.0008739;
RA Lu C., Ding F., Ke A.;
RT "Crystal structure of the S. solfataricus archaeal exosome reveals
RT conformational flexibility in the RNA-binding ring.";
RL PLoS ONE 5:E8739-E8739(2010).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF MUTANT ALA-182 IN COMPLEX WITH
RP RRP42 AND RRP4, AND SUBUNIT.
RX PubMed=23319881; DOI=10.1155/2012/721869;
RA Lorentzen E., Conti E.;
RT "Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states
RT of the phosphorolytic reaction.";
RL Archaea 2012:721869-721869(2012).
CC -!- FUNCTION: Catalytic component of the exosome, which is a complex
CC involved in RNA degradation. Has 3'->5' exoribonuclease activity. Can
CC also synthesize heteromeric RNA-tails. Binds RNA. {ECO:0000255|HAMAP-
CC Rule:MF_00591, ECO:0000269|PubMed:15951817,
CC ECO:0000269|PubMed:17380186, ECO:0000269|PubMed:20488184}.
CC -!- SUBUNIT: Component of the archaeal exosome complex. Forms a hexameric
CC ring-like arrangement composed of 3 Rrp41-Rrp42 heterodimers. The
CC hexameric ring associates with a trimer of Rrp4 and/or Csl4 subunits.
CC {ECO:0000255|HAMAP-Rule:MF_00591, ECO:0000269|PubMed:15951817,
CC ECO:0000269|PubMed:16285928, ECO:0000269|PubMed:17380186,
CC ECO:0000269|PubMed:20090900, ECO:0000269|PubMed:20488184,
CC ECO:0000269|PubMed:23319881}.
CC -!- INTERACTION:
CC Q9UXC2; Q9UXC0: rrp42; NbExp=3; IntAct=EBI-7981302, EBI-9009550;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00591}.
CC -!- SIMILARITY: Belongs to the RNase PH family. Rrp41 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00591}.
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DR EMBL; Y18930; CAB57569.1; -; Genomic_DNA.
DR EMBL; AE006641; AAK41031.1; -; Genomic_DNA.
DR PIR; H90221; H90221.
DR PDB; 2BR2; X-ray; 2.80 A; B/D/F/H/J/L/N/P/R/T/V/X=1-248.
DR PDB; 2C37; X-ray; 2.80 A; B/D/F/H/J/L/N/P/R/T/V/X=1-248.
DR PDB; 2C38; X-ray; 3.10 A; B/D/F/H/J/L/N/P/R/T/V/X=1-248.
DR PDB; 2C39; X-ray; 3.30 A; B/D/F/H/J/L/N/P/R/T/V/X=1-248.
DR PDB; 2JE6; X-ray; 1.60 A; B=1-248.
DR PDB; 2JEA; X-ray; 2.33 A; B=1-248.
DR PDB; 2JEB; X-ray; 2.40 A; B=1-248.
DR PDB; 3L7Z; X-ray; 2.41 A; B/E/H=4-248.
DR PDB; 4BA1; X-ray; 1.80 A; B=1-248.
DR PDB; 4BA2; X-ray; 2.50 A; B=1-248.
DR PDBsum; 2BR2; -.
DR PDBsum; 2C37; -.
DR PDBsum; 2C38; -.
DR PDBsum; 2C39; -.
DR PDBsum; 2JE6; -.
DR PDBsum; 2JEA; -.
DR PDBsum; 2JEB; -.
DR PDBsum; 3L7Z; -.
DR PDBsum; 4BA1; -.
DR PDBsum; 4BA2; -.
DR AlphaFoldDB; Q9UXC2; -.
DR SMR; Q9UXC2; -.
DR DIP; DIP-58154N; -.
DR IntAct; Q9UXC2; 2.
DR MINT; Q9UXC2; -.
DR STRING; 273057.SSO0735; -.
DR EnsemblBacteria; AAK41031; AAK41031; SSO0735.
DR KEGG; sso:SSO0735; -.
DR PATRIC; fig|273057.12.peg.731; -.
DR eggNOG; arCOG01575; Archaea.
DR HOGENOM; CLU_063514_0_0_2; -.
DR InParanoid; Q9UXC2; -.
DR OMA; KGKGQGW; -.
DR PhylomeDB; Q9UXC2; -.
DR EvolutionaryTrace; Q9UXC2; -.
DR Proteomes; UP000001974; Chromosome.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR CDD; cd11366; RNase_PH_archRRP41; 1.
DR Gene3D; 3.30.230.70; -; 1.
DR HAMAP; MF_00591; Exosome_Rrp41; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR015847; ExoRNase_PH_dom2.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR011807; Rrp41.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
DR TIGRFAMs; TIGR02065; ECX1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exonuclease; Exosome; Hydrolase; Nuclease;
KW Reference proteome.
FT CHAIN 1..248
FT /note="Exosome complex component Rrp41"
FT /id="PRO_0000139991"
FT MUTAGEN 98
FT /note="R->E: Abolishes exoribonuclease activity; when
FT associated with E-99."
FT /evidence="ECO:0000269|PubMed:16285928"
FT MUTAGEN 99
FT /note="R->E: Abolishes exoribonuclease activity; when
FT associated with E-98."
FT /evidence="ECO:0000269|PubMed:16285928"
FT MUTAGEN 182
FT /note="D->A: Abolishes both exoribonuclease and
FT polyadenylation activities."
FT /evidence="ECO:0000269|PubMed:15951817"
FT HELIX 2..4
FT /evidence="ECO:0007829|PDB:2C39"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:2C39"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 39..49
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 52..63
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 76..83
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 87..90
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 98..112
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 123..133
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 138..152
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 157..159
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 162..169
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 172..176
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 179..184
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 185..194
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 199..207
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 211..237
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:2JE6"
SQ SEQUENCE 248 AA; 27578 MW; EAB2C2C89DD5854C CRC64;
MREMLQVERP KLILDDGKRT DGRKPDELRS IKIELGVLKN ADGSAIFEMG NTKAIAAVYG
PKEMHPRHLS LPDRAVLRVR YHMTPFSTDE RKNPAPSRRE IELSKVIREA LESAVLVELF
PRTAIDVFTE ILQADAGSRL VSLMAASLAL ADAGIPMRDL IAGVAVGKAD GVIILDLNET
EDMWGEADMP IAMMPSLNQV TLFQLNGSMT PDEFRQAFDL AVKGINIIYN LEREALKSKY
VEFKEEGV
