RRP42_SACS2
ID RRP42_SACS2 Reviewed; 275 AA.
AC Q9UXC0;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 119.
DE RecName: Full=Exosome complex component Rrp42 {ECO:0000255|HAMAP-Rule:MF_00622};
GN Name=rrp42 {ECO:0000255|HAMAP-Rule:MF_00622}; OrderedLocusNames=SSO0732;
GN ORFNames=C20_023;
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 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, AND SUBUNIT.
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 [6]
RP INTERACTION WITH EXOSOME.
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 [7]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP41, SUBUNIT, AND
RP MUTAGENESIS OF ARG-112 AND ARG-116.
RX PubMed=16285928; DOI=10.1016/j.molcel.2005.10.020;
RA Lorentzen E., Conti E.;
RT "Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage
RT by an exosome RNase PH core.";
RL Mol. Cell 20:473-481(2005).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP41, FUNCTION,
RP SUBUNIT, AND MUTAGENESIS OF GLU-218.
RX PubMed=15951817; DOI=10.1038/nsmb952;
RA Lorentzen E., Walter P., Fribourg S., Evguenieva-Hackenberg E., Klug G.,
RA Conti E.;
RT "The archaeal exosome core is a hexameric ring structure with three
RT catalytic subunits.";
RL Nat. Struct. Mol. Biol. 12:575-581(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP4, AND
RP SUBUNIT.
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 [10]
RP X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP4.
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 [11]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP4, AND
RP SUBUNIT.
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. Contributes to the structuring of the
CC Rrp41 active site. {ECO:0000255|HAMAP-Rule:MF_00622,
CC ECO:0000269|PubMed:15951817, ECO:0000269|PubMed:20488184}.
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:15951817,
CC ECO:0000269|PubMed:16285928, ECO:0000269|PubMed:17380186,
CC ECO:0000269|PubMed:20090900, ECO:0000269|PubMed:20488184,
CC ECO:0000269|PubMed:23319881}.
CC -!- INTERACTION:
CC Q9UXC0; Q9UXC2: rrp41; NbExp=3; IntAct=EBI-9009550, EBI-7981302;
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; Y18930; CAB57571.1; -; Genomic_DNA.
DR EMBL; AE006641; AAK41030.1; -; Genomic_DNA.
DR PIR; G90221; G90221.
DR RefSeq; WP_009991305.1; NC_002754.1.
DR PDB; 2BR2; X-ray; 2.80 A; A/C/E/G/I/K/M/O/Q/S/U/W=1-275.
DR PDB; 2C37; X-ray; 2.80 A; A/C/E/G/I/K/M/O/Q/S/U/W=1-275.
DR PDB; 2C38; X-ray; 3.10 A; A/C/E/G/I/K/M/O/Q/S/U/W=1-275.
DR PDB; 2C39; X-ray; 3.30 A; A/C/E/G/I/K/M/O/Q/S/U/W=1-275.
DR PDB; 2JE6; X-ray; 1.60 A; A=1-275.
DR PDB; 2JEA; X-ray; 2.33 A; A=1-275.
DR PDB; 2JEB; X-ray; 2.40 A; A=1-275.
DR PDB; 3L7Z; X-ray; 2.41 A; A/D/G=1-275.
DR PDB; 4BA1; X-ray; 1.80 A; A=1-275.
DR PDB; 4BA2; X-ray; 2.50 A; A=1-275.
DR PDBsum; 2BR2; -.
DR PDBsum; 2C37; -.
DR PDBsum; 2C38; -.
DR PDBsum; 2C39; -.
DR PDBsum; 2JE6; -.
DR PDBsum; 2JEA; -.
DR PDBsum; 2JEB; -.
DR PDBsum; 3L7Z; -.
DR PDBsum; 4BA1; -.
DR PDBsum; 4BA2; -.
DR AlphaFoldDB; Q9UXC0; -.
DR SMR; Q9UXC0; -.
DR DIP; DIP-60492N; -.
DR IntAct; Q9UXC0; 1.
DR STRING; 273057.SSO0732; -.
DR EnsemblBacteria; AAK41030; AAK41030; SSO0732.
DR GeneID; 44129730; -.
DR KEGG; sso:SSO0732; -.
DR PATRIC; fig|273057.12.peg.730; -.
DR eggNOG; arCOG01574; Archaea.
DR HOGENOM; CLU_038194_0_0_2; -.
DR InParanoid; Q9UXC0; -.
DR OMA; PESVFEM; -.
DR PhylomeDB; Q9UXC0; -.
DR EvolutionaryTrace; Q9UXC0; -.
DR Proteomes; UP000001974; Chromosome.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
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..275
FT /note="Exosome complex component Rrp42"
FT /id="PRO_0000140006"
FT MUTAGEN 112
FT /note="R->E: Abolishes exoribonuclease activity of the
FT complex; when associated with E-116."
FT /evidence="ECO:0000269|PubMed:16285928"
FT MUTAGEN 116
FT /note="R->E: Abolishes exoribonuclease activity of the
FT complex; when associated with E-112."
FT /evidence="ECO:0000269|PubMed:16285928"
FT MUTAGEN 218
FT /note="E->A: Does not change activity."
FT /evidence="ECO:0000269|PubMed:15951817"
FT HELIX 13..19
FT /evidence="ECO:0007829|PDB:2JE6"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:2C38"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 50..58
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 61..72
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:2C37"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:3L7Z"
FT STRAND 83..90
FT /evidence="ECO:0007829|PDB:2JE6"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:2JEA"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:2JEB"
FT HELIX 105..120
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 126..129
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:2JE6"
FT TURN 133..135
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 136..148
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 153..166
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 169..174
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 181..190
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:2JEA"
FT STRAND 198..205
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 208..212
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:2JE6"
FT STRAND 222..229
FT /evidence="ECO:0007829|PDB:2JE6"
FT TURN 231..233
FT /evidence="ECO:0007829|PDB:3L7Z"
FT STRAND 235..244
FT /evidence="ECO:0007829|PDB:2JE6"
FT HELIX 248..273
FT /evidence="ECO:0007829|PDB:2JE6"
SQ SEQUENCE 275 AA; 30194 MW; 4188C9D6928A144C CRC64;
MSSTPSNQNI IPIIKKESIV SLFEKGIRQD GRKLTDYRPL SITLDYAKKA DGSALVKLGT
TMVLAGTKLE IDKPYEDTPN QGNLIVNVEL LPLAYETFEP GPPDENAIEL ARVVDRSLRD
SKALDLTKLV IEPGKSVWTV WLDVYVLDYG GNVLDACTLA SVAALYNTKV YKVEQHSNGI
SVNKNEVVGK LPLNYPVVTI SVAKVDKYLV VDPDLDEESI MDAKISFSYT PDLKIVGIQK
SGKGSMSLQD IDQAENTARS TAVKLLEELK KHLGI
