RRP4_ARCFU
ID RRP4_ARCFU Reviewed; 223 AA.
AC O29758;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=Exosome complex component Rrp4 {ECO:0000255|HAMAP-Rule:MF_00623};
GN Name=rrp4 {ECO:0000255|HAMAP-Rule:MF_00623}; OrderedLocusNames=AF_0492;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2]
RP FUNCTION, AND SUBUNIT.
RX PubMed=20392821; DOI=10.1093/nar/gkq238;
RA Hartung S., Niederberger T., Hartung M., Tresch A., Hopfner K.P.;
RT "Quantitative analysis of processive RNA degradation by the archaeal RNA
RT exosome.";
RL Nucleic Acids Res. 38:5166-5176(2010).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42,
RP FUNCTION, SUBUNIT, AND DOMAIN.
RX PubMed=16285927; DOI=10.1016/j.molcel.2005.10.018;
RA Buttner K., Wenig K., Hopfner K.P.;
RT "Structural framework for the mechanism of archaeal exosomes in RNA
RT processing.";
RL Mol. Cell 20:461-471(2005).
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 (Probable). {ECO:0000305|PubMed:16285927,
CC ECO:0000305|PubMed:20392821}.
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:16285927,
CC ECO:0000269|PubMed:20392821}.
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.
CC {ECO:0000269|PubMed:16285927}.
CC -!- SIMILARITY: Belongs to the RRP4 family. {ECO:0000255|HAMAP-
CC Rule:MF_00623}.
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DR EMBL; AE000782; AAB90745.1; -; Genomic_DNA.
DR PIR; D69311; D69311.
DR RefSeq; WP_010877999.1; NC_000917.1.
DR PDB; 2BA0; X-ray; 2.70 A; A/B/C=1-223.
DR PDBsum; 2BA0; -.
DR AlphaFoldDB; O29758; -.
DR SMR; O29758; -.
DR STRING; 224325.AF_0492; -.
DR EnsemblBacteria; AAB90745; AAB90745; AF_0492.
DR GeneID; 24794032; -.
DR KEGG; afu:AF_0492; -.
DR eggNOG; arCOG00678; Archaea.
DR HOGENOM; CLU_071769_0_0_2; -.
DR OMA; GPYIPEV; -.
DR OrthoDB; 93052at2157; -.
DR PhylomeDB; O29758; -.
DR EvolutionaryTrace; O29758; -.
DR Proteomes; UP000002199; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000178; C:exosome (RNase complex); IEA:UniProtKB-KW.
DR GO; GO:0008143; F:poly(A) binding; IEA:InterPro.
DR GO; GO:0006401; P:RNA catabolic process; IEA:UniProtKB-UniRule.
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; IPR004087; KH_dom.
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 Pfam; PF00575; S1; 1.
DR SMART; SM00322; KH; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
DR PROSITE; PS50084; KH_TYPE_1; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Reference proteome; RNA-binding.
FT CHAIN 1..223
FT /note="Exosome complex component Rrp4"
FT /id="PRO_0000050145"
FT DOMAIN 58..127
FT /note="S1 motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00623"
FT DOMAIN 135..193
FT /note="KH"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00623"
FT STRAND 10..13
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 22..25
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 33..39
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 44..48
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 60..68
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 70..76
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 83..86
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 108..116
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 132..141
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 147..151
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 156..165
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 168..171
FT /evidence="ECO:0007829|PDB:2BA0"
FT STRAND 175..181
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 183..198
FT /evidence="ECO:0007829|PDB:2BA0"
FT HELIX 205..218
FT /evidence="ECO:0007829|PDB:2BA0"
SQ SEQUENCE 223 AA; 24725 MW; A11B7F1A26972833 CRC64;
MRKIVLPGDL LSTNPRAAGY GTYVEGGKVY AKIIGLFDQT ETHVRVIPLK GRYTPSVGDV
VIGIIREVAA NGWAVDIYSP YQAFLPVSEN PEMKPNKKPN EVLDIGDAII AKVLNIDPKM
KVTLTMKDRI CRPIRFGRIV AINPARVPRV IGKKGSMIKL LKSELDVQIV VGQNGLIWVN
GDRRKVSIAE EAIYLIEQEA HTEGLTDRVA EFIKRRKADV GIQ
