RNJ1_STAES
ID RNJ1_STAES Reviewed; 560 AA.
AC Q8CT16;
DT 15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Ribonuclease J 1 {ECO:0000255|HAMAP-Rule:MF_01491};
DE Short=RNase J1 {ECO:0000255|HAMAP-Rule:MF_01491};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01491};
GN Name=rnj1 {ECO:0000255|HAMAP-Rule:MF_01491}; OrderedLocusNames=SE_0787;
OS Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=176280;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12228 / FDA PCI 1200;
RX PubMed=12950922; DOI=10.1046/j.1365-2958.2003.03671.x;
RA Zhang Y.-Q., Ren S.-X., Li H.-L., Wang Y.-X., Fu G., Yang J., Qin Z.-Q.,
RA Miao Y.-G., Wang W.-Y., Chen R.-S., Shen Y., Chen Z., Yuan Z.-H.,
RA Zhao G.-P., Qu D., Danchin A., Wen Y.-M.;
RT "Genome-based analysis of virulence genes in a non-biofilm-forming
RT Staphylococcus epidermidis strain (ATCC 12228).";
RL Mol. Microbiol. 49:1577-1593(2003).
CC -!- FUNCTION: An RNase that has 5'-3' exonuclease and possibly
CC endoonuclease activity. Involved in maturation of rRNA and in some
CC organisms also mRNA maturation and/or decay (By similarity).
CC {ECO:0000250}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01491};
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};
CC -!- SUBUNIT: Homodimer, may be a subunit of the RNA degradosome.
CC {ECO:0000255|HAMAP-Rule:MF_01491}.
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; AE015929; AAO04384.1; -; Genomic_DNA.
DR RefSeq; NP_764342.1; NC_004461.1.
DR RefSeq; WP_001831649.1; NZ_WBME01000031.1.
DR PDB; 6K6S; X-ray; 2.99 A; A/B=1-560.
DR PDBsum; 6K6S; -.
DR AlphaFoldDB; Q8CT16; -.
DR SMR; Q8CT16; -.
DR STRING; 176280.SE_0787; -.
DR EnsemblBacteria; AAO04384; AAO04384; SE_0787.
DR GeneID; 50019074; -.
DR KEGG; sep:SE_0787; -.
DR PATRIC; fig|176280.10.peg.760; -.
DR eggNOG; COG0595; Bacteria.
DR HOGENOM; CLU_008727_3_1_9; -.
DR OMA; KNTCVFE; -.
DR Proteomes; UP000001411; 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: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 InterPro; IPR001587; RNase_J_CS.
DR Pfam; PF00753; Lactamase_B; 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; PS01292; UPF0036; 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..560
FT /note="Ribonuclease J 1"
FT /id="PRO_0000286854"
FT BINDING 74
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 BINDING 76
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 BINDING 78
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 BINDING 79
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 BINDING 142
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 BINDING 164
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 BINDING 164
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 BINDING 364..368
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 390
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 STRAND 9..15
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 24..29
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 49..55
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 67..72
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 84..89
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 98..110
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 119..121
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 197..200
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 208..219
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 235..247
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 251..254
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 264..267
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 275..277
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 282..287
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 293..297
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 304..306
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 307..312
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 326..329
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 338..351
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 354..356
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 358..362
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 371..380
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 383..386
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 389..391
FT /evidence="ECO:0007829|PDB:6K6S"
FT HELIX 393..404
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 405..407
FT /evidence="ECO:0007829|PDB:6K6S"
FT TURN 410..412
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 420..425
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 428..430
FT /evidence="ECO:0007829|PDB:6K6S"
FT STRAND 439..443
FT /evidence="ECO:0007829|PDB:6K6S"
SQ SEQUENCE 560 AA; 62051 MW; C517FE6FD8F6B1EE CRC64;
MKQLHSNEVG VYALGGLGEV GKNTYAVEYK DEIVIIDAGI KFPDDNLLGI DYVIPDYTYL
EQNQDKIVGL FITHGHEDHI GGVPFLLKQI NVPIYGGPLA LGLIRNKLEE HHLLRTTELH
EIDESSVIKS KHFEISFYLT THSIPEAYGV IVDTPEGKIV HTGDFKFDFT PVGEPANIAK
MAQLGHEGVL CLLSDSTNAL VPDFTLSERE VGQNVDKIFR NCKGRIIFAT FASNIYRVQQ
AVEAAIKYNR KIVTFGRSME NNIKIGMELG YIKAPPETFI EPNKINSVPK HELLILCTGS
QGEPMAALSR IANGTHKQIK IIPEDTVVFS SSPIPGNTKS INRTINALYK AGADVIHSKI
SNIHTSGHGS QGDQQLMLRL IQPKYFLPIH GEYRMLKAHG ETGVQCGVDE DNVFIFDIGD
VLALTHDSAR KAGRIPSGNV LVDGSGIGDI GNVVIRDRKL LSEEGLVIVV VSIDFNTNKL
LSGPDIISRG FVYMRESGQL IYDAQRKIKG DVISKLNSNK DIQWHQIKSS IIETLHPYLY
EKTARKPMIL PVIMKVNEDK
