RRP4_SACS2
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 25-MAY-2022, entry version 121.
DE RecName: Full=Exosome complex component Rrp4 {ECO:0000255|HAMAP-Rule:MF_00623};
GN Name=rrp4 {ECO:0000255|HAMAP-Rule:MF_00623}; OrderedLocusNames=SSO0736;
GN ORFNames=C20_026;
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 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 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 OMA; GPYIPEV; -.
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 Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1370.10; -; 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; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR PANTHER; PTHR21321; PTHR21321; 1.
DR Pfam; PF15985; KH_6; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 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
