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 27-MAR-2024, entry version 121. 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}; GN OrderedLocusNames=SSO0735; OS Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) OS (Sulfolobus solfataricus). OC Archaea; Thermoproteota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 PaxDb; 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 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'-RNA exonuclease 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; GHMP Kinase, N-terminal domain; 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_Su5_D2-typ_SF. DR InterPro; IPR011807; Rrp41. DR NCBIfam; TIGR02065; ECX1; 1. DR PANTHER; PTHR11953; EXOSOME COMPLEX COMPONENT; 1. DR PANTHER; PTHR11953:SF2; EXOSOME COMPLEX COMPONENT MTR3; 1. DR Pfam; PF01138; RNase_PH; 1. DR Pfam; PF03725; RNase_PH_C; 1. DR SUPFAM; SSF55666; Ribonuclease PH domain 2-like; 1. DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 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 //