RRP42_ARCFU
ID RRP42_ARCFU Reviewed; 259 AA.
AC O29756;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 25-MAY-2022, entry version 114.
DE RecName: Full=Exosome complex component Rrp42 {ECO:0000255|HAMAP-Rule:MF_00622};
GN Name=rrp42 {ECO:0000255|HAMAP-Rule:MF_00622}; OrderedLocusNames=AF_0494;
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 X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RRP41; RRP4 AND
RP CSL4, AND SUBUNIT.
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).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH RRP41 AND CSL4, AND
RP 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).
CC -!- FUNCTION: Non-catalytic component of the exosome, which is a complex
CC involved in RNA degradation. Contributes to the structuring of the
CC Rrp41 active site. {ECO:0000255|HAMAP-Rule:MF_00622}.
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_00622, ECO:0000269|PubMed:16285927,
CC ECO:0000269|PubMed:20392821}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00622}.
CC -!- SIMILARITY: Belongs to the RNase PH family. Rrp42 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00622}.
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DR EMBL; AE000782; AAB90743.1; -; Genomic_DNA.
DR PIR; F69311; F69311.
DR RefSeq; WP_010878001.1; NC_000917.1.
DR PDB; 2BA0; X-ray; 2.70 A; G/H/I=1-259.
DR PDB; 2BA1; X-ray; 2.70 A; G/H/I=1-259.
DR PDB; 3M7N; X-ray; 2.40 A; G/H/I=1-259.
DR PDB; 3M85; X-ray; 3.00 A; G/H/I=1-259.
DR PDBsum; 2BA0; -.
DR PDBsum; 2BA1; -.
DR PDBsum; 3M7N; -.
DR PDBsum; 3M85; -.
DR AlphaFoldDB; O29756; -.
DR SMR; O29756; -.
DR STRING; 224325.AF_0494; -.
DR EnsemblBacteria; AAB90743; AAB90743; AF_0494.
DR GeneID; 24794034; -.
DR KEGG; afu:AF_0494; -.
DR eggNOG; arCOG01574; Archaea.
DR HOGENOM; CLU_038194_0_0_2; -.
DR OMA; PESVFEM; -.
DR OrthoDB; 64101at2157; -.
DR PhylomeDB; O29756; -.
DR EvolutionaryTrace; O29756; -.
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:0006401; P:RNA catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd11365; RNase_PH_archRRP42; 1.
DR Gene3D; 3.30.230.70; -; 1.
DR HAMAP; MF_00622; Exosome_Rrp42; 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; IPR020869; Rrp42_archaea.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Reference proteome.
FT CHAIN 1..259
FT /note="Exosome complex component Rrp42"
FT /id="PRO_0000139996"
FT HELIX 5..19
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 35..39
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 45..53
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 56..67
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 78..84
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:3M85"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 100..115
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:3M7N"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 131..143
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 148..161
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 185..192
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 204..207
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 211..216
FT /evidence="ECO:0007829|PDB:3M7N"
FT STRAND 222..230
FT /evidence="ECO:0007829|PDB:3M7N"
FT HELIX 235..254
FT /evidence="ECO:0007829|PDB:3M7N"
SQ SEQUENCE 259 AA; 28647 MW; E8289D46F9DDCCB3 CRC64;
MPEDILVDIK RDYVLSKLRD NERIDGRGFD EFRKVEIIPN VIEKAEGSAL VKLGDTQVVV
GVKMQPGEPY PDTPDRGVII VNAELVPLAS PTFEPGPPDE NSIELARVVD RGIRESEAVD
LSKLVIEEGE KVWIVFVDIH ALDDDGNLLD ASALAAIAAL MNTKVPAERF DLGEDYLLPV
RDLPVSVTSL IVGNKYLVDP SREEMSVGDT TLTITTDKDD NVVAMQKSGG YLLDEKLFDE
LLDVSINCAR KLREKFKEI
