ID   RRP4_SACS2              Reviewed;         249 AA.
AC   Q9UXC4;
DT   25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   27-MAR-2024, entry version 128.
DE   RecName: Full=Exosome complex component Rrp4 {ECO:0000255|HAMAP-Rule:MF_00623};
GN   Name=rrp4 {ECO:0000255|HAMAP-Rule:MF_00623};
GN   OrderedLocusNames=SSO0736; ORFNames=C20_026;
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   FUNCTION, AND 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.
RC   STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX   PubMed=19053279; DOI=10.1021/bi8012214;
RA   Evguenieva-Hackenberg E., Roppelt V., Finsterseifer P., Klug G.;
RT   "Rrp4 and Csl4 are needed for efficient degradation but not for
RT   polyadenylation of synthetic and natural RNA by the archaeal exosome.";
RL   Biochemistry 47:13158-13168(2008).
RN   [6]
RP   FUNCTION.
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   [7]
RP   SUBUNIT, AND DOMAIN.
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   [8]
RP   X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42,
RP   SUBUNIT, AND DOMAIN.
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   [9]
RP   X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42, AND
RP   SUBUNIT.
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   [10]
RP   X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42.
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: Non-catalytic component of the exosome, which is a complex
CC       involved in RNA degradation. Increases the RNA binding and the
CC       efficiency of RNA degradation. Confers strong poly(A) specificity to
CC       the exosome. {ECO:0000255|HAMAP-Rule:MF_00623,
CC       ECO:0000269|PubMed:17078816, ECO:0000269|PubMed:19053279,
CC       ECO:0000269|PubMed:20488184}.
CC   -!- SUBUNIT: Component of the archaeal exosome complex. Forms a trimer of
CC       Rrp4 and/or Csl4 subunits. The trimer associates with a hexameric ring-
CC       like arrangement composed of 3 Rrp41-Rrp42 heterodimers.
CC       {ECO:0000255|HAMAP-Rule:MF_00623, ECO:0000269|PubMed:17380186,
CC       ECO:0000269|PubMed:20090900, ECO:0000269|PubMed:22503705,
CC       ECO:0000269|PubMed:23319881}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00623}.
CC   -!- DOMAIN: Contains an N-terminal domain that mediates interactions with
CC       the hexameric ring, a central S1 domain and a C-terminal KH domain. The
CC       KH domain is required for efficient RNA degradation, but is not
CC       responsible for poly(A) preference. {ECO:0000269|PubMed:17380186,
CC       ECO:0000269|PubMed:22503705}.
CC   -!- SIMILARITY: Belongs to the RRP4 family. {ECO:0000255|HAMAP-
CC       Rule:MF_00623}.
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DR   EMBL; Y18930; CAB57567.1; -; Genomic_DNA.
DR   EMBL; AE006641; AAK41032.1; -; Genomic_DNA.
DR   PIR; A99222; A99222.
DR   PDB; 2JE6; X-ray; 1.60 A; I=1-249.
DR   PDB; 2JEA; X-ray; 2.33 A; I=1-249.
DR   PDB; 2JEB; X-ray; 2.40 A; I=1-249.
DR   PDB; 3L7Z; X-ray; 2.41 A; C/F/I=1-249.
DR   PDB; 4BA1; X-ray; 1.80 A; I=1-249.
DR   PDB; 4BA2; X-ray; 2.50 A; I=1-249.
DR   PDBsum; 2JE6; -.
DR   PDBsum; 2JEA; -.
DR   PDBsum; 2JEB; -.
DR   PDBsum; 3L7Z; -.
DR   PDBsum; 4BA1; -.
DR   PDBsum; 4BA2; -.
DR   AlphaFoldDB; Q9UXC4; -.
DR   SMR; Q9UXC4; -.
DR   STRING; 273057.SSO0736; -.
DR   PaxDb; 273057-SSO0736; -.
DR   EnsemblBacteria; AAK41032; AAK41032; SSO0736.
DR   KEGG; sso:SSO0736; -.
DR   PATRIC; fig|273057.12.peg.732; -.
DR   eggNOG; arCOG00678; Archaea.
DR   HOGENOM; CLU_071769_0_0_2; -.
DR   InParanoid; Q9UXC4; -.
DR   PhylomeDB; Q9UXC4; -.
DR   EvolutionaryTrace; Q9UXC4; -.
DR   Proteomes; UP000001974; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0000178; C:exosome (RNase complex); IBA:GO_Central.
DR   GO; GO:0008143; F:poly(A) binding; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR   GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central.
DR   GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
DR   GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR   GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
DR   GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR   CDD; cd22524; KH-I_Rrp4_prokar; 1.
DR   CDD; cd05789; S1_Rrp4; 1.
DR   Gene3D; 2.40.50.100; -; 1.
DR   Gene3D; 3.30.1370.10; K Homology domain, type 1; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   HAMAP; MF_00623; Exosome_Rrp4; 1.
DR   InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
DR   InterPro; IPR004088; KH_dom_type_1.
DR   InterPro; IPR036612; KH_dom_type_1_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR023474; Rrp4.
DR   InterPro; IPR048565; RRP4_S1.
DR   InterPro; IPR003029; S1_domain.
DR   PANTHER; PTHR21321:SF1; EXOSOME COMPLEX COMPONENT RRP40; 1.
DR   PANTHER; PTHR21321; PNAS-3 RELATED; 1.
DR   Pfam; PF15985; KH_6; 1.
DR   SMART; SM00316; S1; 1.
DR   SUPFAM; SSF54791; Eukaryotic type KH-domain (KH-domain type I); 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF110324; Ribosomal L27 protein-like; 1.
DR   PROSITE; PS50126; S1; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Exosome; Reference proteome; RNA-binding.
FT   CHAIN           1..249
FT                   /note="Exosome complex component Rrp4"
FT                   /id="PRO_0000050156"
FT   DOMAIN          73..144
FT                   /note="S1 motif"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00623"
FT   DOMAIN          154..211
FT                   /note="KH"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00623"
FT   STRAND          8..10
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          15..17
FT                   /evidence="ECO:0007829|PDB:4BA1"
FT   STRAND          22..26
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          36..39
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          42..45
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          47..54
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          57..63
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          75..83
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          85..91
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          93..96
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          98..101
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   HELIX           102..106
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          117..119
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          125..134
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          137..142
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          156..158
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   HELIX           161..163
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   HELIX           164..168
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   HELIX           170..172
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   HELIX           173..179
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   STRAND          187..189
FT                   /evidence="ECO:0007829|PDB:3L7Z"
FT   STRAND          192..195
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   TURN            201..206
FT                   /evidence="ECO:0007829|PDB:4BA1"
FT   HELIX           208..211
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   TURN            212..219
FT                   /evidence="ECO:0007829|PDB:2JE6"
FT   TURN            224..227
FT                   /evidence="ECO:0007829|PDB:3L7Z"
FT   HELIX           232..235
FT                   /evidence="ECO:0007829|PDB:3L7Z"
FT   TURN            236..238
FT                   /evidence="ECO:0007829|PDB:3L7Z"
SQ   SEQUENCE   249 AA;  27998 MW;  A36AD0CA0363D4B8 CRC64;
     MNMSQSQKIV LQPRSIVVPG ELLAEGEFQI PWSPYILKIN SKYYSTVVGL FDVKDTQFEV
     IPLEGSFYYP KINDIVIGLV EDVEIYGWVV DIKAPYKAYL PASNLLGRSI NVGEDLRRYL
     DVGDYVIARI ENFDRSIDPV LSVKGKDLGR VSNGIVIDIM PVKVPRVIGK NKSMYETLTS
     KSGCSIFVAN NGRIWATCPS RFSEEILIEA IRKIENESHI KGLTDRIKQF IEEKLGERNA
     SSGETKTNS
//