RNJ_THET2
ID RNJ_THET2 Reviewed; 573 AA.
AC Q72JJ7;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Ribonuclease J {ECO:0000255|HAMAP-Rule:MF_01491};
DE Short=RNase J {ECO:0000255|HAMAP-Rule:MF_01491};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01491};
GN Name=rnj {ECO:0000255|HAMAP-Rule:MF_01491}; OrderedLocusNames=TT_C0775;
OS Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=262724;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=15064768; DOI=10.1038/nbt956;
RA Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H.,
RA Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C.,
RA Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P.,
RA Kramer W., Merkl R., Gottschalk G., Fritz H.-J.;
RT "The genome sequence of the extreme thermophile Thermus thermophilus.";
RL Nat. Biotechnol. 22:547-553(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 20-573 IN CLOSED CONFROMATION IN
RP COMPLEX WITH ZINC WITH OR WITHOUT SUBSTRATE, FUNCTION AS AN ENDONUCLEASE,
RP AND SUBUNIT.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=18204464; DOI=10.1038/nsmb.1376;
RA Li de la Sierra-Gallay I., Zig L., Jamalli A., Putzer H.;
RT "Structural insights into the dual activity of RNase J.";
RL Nat. Struct. Mol. Biol. 15:206-212(2008).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 20-572 IN CLOSED CONFORMATION IN
RP COMPLEX WITH ZINC AND SUBSTRATE, RNA-BINDING, AND MUTAGENESIS OF HIS-95.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=21893286; DOI=10.1016/j.str.2011.06.018;
RA Dorleans A., Li de la Sierra-Gallay I., Piton J., Zig L., Gilet L.,
RA Putzer H., Condon C.;
RT "Molecular basis for the recognition and cleavage of RNA by the
RT bifunctional 5'-3' exo/endoribonuclease RNase J.";
RL Structure 19:1252-1261(2011).
CC -!- FUNCTION: An RNase that has endonuclease and possibly 5'-3' exonuclease
CC activity. Probably involved in maturation of rRNA and in some organisms
CC also mRNA maturation and/or decay. {ECO:0000269|PubMed:18204464}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01491,
CC ECO:0000269|PubMed:21893286};
CC Note=Binds up to 2 Zn(2+) ions per subunit. It is not clear if Zn(2+)
CC or Mg(2+) is physiologically important. {ECO:0000255|HAMAP-
CC Rule:MF_01491, ECO:0000269|PubMed:21893286};
CC -!- SUBUNIT: Homodimer (Probable). May be a subunit of the RNA degradosome
CC (By similarity). {ECO:0000250, ECO:0000305}.
CC -!- INTERACTION:
CC Q72JJ7; Q72JJ7: rnj; NbExp=3; IntAct=EBI-15680417, EBI-15680417;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01491}.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. RNA-
CC metabolizing metallo-beta-lactamase-like family. Bacterial RNase J
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01491}.
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DR EMBL; AE017221; AAS81121.1; -; Genomic_DNA.
DR RefSeq; WP_011173208.1; NC_005835.1.
DR PDB; 3BK1; X-ray; 2.33 A; A=20-573.
DR PDB; 3BK2; X-ray; 2.10 A; A=20-573.
DR PDB; 3T3N; X-ray; 3.09 A; A=20-572.
DR PDB; 3T3O; X-ray; 2.50 A; A=20-572.
DR PDBsum; 3BK1; -.
DR PDBsum; 3BK2; -.
DR PDBsum; 3T3N; -.
DR PDBsum; 3T3O; -.
DR AlphaFoldDB; Q72JJ7; -.
DR SMR; Q72JJ7; -.
DR DIP; DIP-46391N; -.
DR STRING; 262724.TT_C0775; -.
DR EnsemblBacteria; AAS81121; AAS81121; TT_C0775.
DR GeneID; 3169514; -.
DR KEGG; tth:TT_C0775; -.
DR eggNOG; COG0595; Bacteria.
DR HOGENOM; CLU_008727_3_1_0; -.
DR OMA; KNTCVFE; -.
DR OrthoDB; 580619at2; -.
DR BRENDA; 4.6.1.22; 2305.
DR EvolutionaryTrace; Q72JJ7; -.
DR Proteomes; UP000000592; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.10710; -; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR HAMAP; MF_01491; RNase_J_bact; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR InterPro; IPR011108; RMMBL.
DR InterPro; IPR004613; RNase_J.
DR InterPro; IPR042173; RNase_J_2.
DR InterPro; IPR030854; RNase_J_bac.
DR InterPro; IPR041636; RNase_J_C.
DR Pfam; PF12706; Lactamase_B_2; 1.
DR Pfam; PF07521; RMMBL; 1.
DR Pfam; PF17770; RNase_J_C; 1.
DR PIRSF; PIRSF004803; RnjA; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR00649; MG423; 1.
DR PROSITE; PS00216; SUGAR_TRANSPORT_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Exonuclease; Hydrolase;
KW Metal-binding; Nuclease; RNA-binding; rRNA processing; Zinc.
FT CHAIN 1..573
FT /note="Ribonuclease J"
FT /id="PRO_0000429577"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 93
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 97
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 168
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 190
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT BINDING 259..261
FT /ligand="substrate"
FT BINDING 390..394
FT /ligand="substrate"
FT BINDING 416
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491,
FT ECO:0000269|PubMed:21893286"
FT SITE 60
FT /note="Substrate binding"
FT MUTAGEN 95
FT /note="H->A: Catalytically inactive."
FT /evidence="ECO:0000269|PubMed:21893286"
FT STRAND 23..25
FT /evidence="ECO:0007829|PDB:3T3O"
FT STRAND 28..40
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 77..81
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 96..99
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 116..121
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 122..134
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:3T3O"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 152..155
FT /evidence="ECO:0007829|PDB:3BK2"
FT TURN 156..158
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 159..165
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 174..180
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 206..214
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 217..222
FT /evidence="ECO:0007829|PDB:3BK2"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 235..248
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 262..274
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 278..282
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 284..295
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:3T3O"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 319..323
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 331..338
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 352..355
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 364..376
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 380..382
FT /evidence="ECO:0007829|PDB:3BK2"
FT TURN 384..386
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 387..389
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 397..407
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 410..417
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 419..430
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 432..434
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 437..439
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 446..450
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 455..460
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 465..469
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 472..476
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 478..490
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 492..502
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 504..511
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 514..517
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 520..536
FT /evidence="ECO:0007829|PDB:3BK2"
FT HELIX 541..560
FT /evidence="ECO:0007829|PDB:3BK2"
FT STRAND 565..572
FT /evidence="ECO:0007829|PDB:3BK2"
SQ SEQUENCE 573 AA; 64031 MW; 38040323535E392F CRC64;
MENQERKPRR RRRRRPQEGS QGGPQDHVEI IPLGGMGEIG KNITVFRFRD EIFVLDGGLA
FPEEGMPGVD LLIPRVDYLI EHRHKIKAWV LTHGHEDHIG GLPFLLPMIF GKESPVPIYG
ARLTLGLLRG KLEEFGLRPG AFNLKEISPD DRIQVGRYFT LDLFRMTHSI PDNSGVVIRT
PIGTIVHTGD FKLDPTPIDG KVSHLAKVAQ AGAEGVLLLI ADATNAERPG YTPSEMEIAK
ELDRVIGRAP GRVFVTTFAS HIHRIQSVIW AAEKYGRKVA MEGRSMLKFS RIALELGYLK
VKDRLYTLEE VKDLPDHQVL ILATGSQGQP MSVLHRLAFE GHAKMAIKPG DTVILSSSPI
PGNEEAVNRV INRLYALGAY VLYPPTYKVH ASGHASQEEL KLILNLTTPR FFLPWHGEVR
HQMNFKWLAE SMSRPPEKTL IGENGAVYRL TRETFEKVGE VPHGVLYVDG LGVGDITEEI
LADRRHMAEE GLVVITALAG EDPVVEVVSR GFVKAGERLL GEVRRMALEA LKNGVREKKP
LERIRDDIYY PVKKFLKKAT GRDPMILPVV IEG
