RRP42_PYRAB
ID RRP42_PYRAB Reviewed; 274 AA.
AC Q9V118; G8ZJ76;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, 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=PYRAB06110;
GN ORFNames=PAB0421;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) IN COMPLEX WITH RRP41, AND
RP MUTAGENESIS OF LYS-45.
RX PubMed=18353775; DOI=10.1074/jbc.m801005200;
RA Navarro M.V., Oliveira C.C., Zanchin N.I., Guimaraes B.G.;
RT "Insights into the mechanism of progressive RNA degradation by the archaeal
RT exosome.";
RL J. Biol. Chem. 283:14120-14131(2008).
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}.
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; AJ248284; CAB49533.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70003.1; -; Genomic_DNA.
DR PIR; F75181; F75181.
DR RefSeq; WP_010867735.1; NC_000868.1.
DR PDB; 2PNZ; X-ray; 2.14 A; B=1-274.
DR PDB; 2PO0; X-ray; 2.30 A; B=1-274.
DR PDB; 2PO1; X-ray; 1.94 A; B=1-274.
DR PDB; 2PO2; X-ray; 2.41 A; B=1-274.
DR PDBsum; 2PNZ; -.
DR PDBsum; 2PO0; -.
DR PDBsum; 2PO1; -.
DR PDBsum; 2PO2; -.
DR AlphaFoldDB; Q9V118; -.
DR SMR; Q9V118; -.
DR STRING; 272844.PAB0421; -.
DR EnsemblBacteria; CAB49533; CAB49533; PAB0421.
DR GeneID; 1495516; -.
DR KEGG; pab:PAB0421; -.
DR PATRIC; fig|272844.11.peg.649; -.
DR eggNOG; arCOG01574; Archaea.
DR HOGENOM; CLU_038194_0_0_2; -.
DR OMA; PESVFEM; -.
DR OrthoDB; 64101at2157; -.
DR PhylomeDB; Q9V118; -.
DR EvolutionaryTrace; Q9V118; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; 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.
FT CHAIN 1..274
FT /note="Exosome complex component Rrp42"
FT /id="PRO_0000140001"
FT MUTAGEN 45
FT /note="K->A: Does not affect ring assembly, but decreases
FT RNA degradation."
FT /evidence="ECO:0000269|PubMed:18353775"
FT HELIX 10..20
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 46..54
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 57..68
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 79..86
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 101..115
FT /evidence="ECO:0007829|PDB:2PO1"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 122..125
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 126..128
FT /evidence="ECO:0007829|PDB:2PO1"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 132..144
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 149..163
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:2PO1"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 178..186
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 194..201
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 211..216
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 218..225
FT /evidence="ECO:0007829|PDB:2PO1"
FT STRAND 231..239
FT /evidence="ECO:0007829|PDB:2PO1"
FT HELIX 244..272
FT /evidence="ECO:0007829|PDB:2PO1"
SQ SEQUENCE 274 AA; 29952 MW; 01EFAA68DD57CAEF CRC64;
MSDNEIVAGI MRDHIINLLK EGKRIDDRGF EDYRPIEIEV GVIEKAEGSA LVKLGSTQVL
VGIKTSLGEP FPDTPNMGVM TTNVELVPLA SPTFEPGPPD ERAIELARVI DRGIRESKAL
NLEKMVIVPG KIVRVVFIDV HVLDHDGNLM DAIGIAAIAA LLNARVPKVR YNEETGEVET
LDETEPLPVE KIPVPVTFAK IGNILVVDPS LDEELVMDGK ITITTDETGH ISAVQKSEGG
AFKLEEVMYA VETAFKKAEE IRKLILEAVE KAKQ
