RNT_ECOLI
ID RNT_ECOLI Reviewed; 215 AA.
AC P30014; P76896;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1993, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Ribonuclease T {ECO:0000255|HAMAP-Rule:MF_00157};
DE EC=3.1.13.- {ECO:0000255|HAMAP-Rule:MF_00157};
DE AltName: Full=Exoribonuclease T {ECO:0000255|HAMAP-Rule:MF_00157};
DE Short=RNase T {ECO:0000255|HAMAP-Rule:MF_00157};
GN Name=rnt {ECO:0000255|HAMAP-Rule:MF_00157};
GN OrderedLocusNames=b1652, JW1644;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CATALYTIC ACTIVITY.
RC STRAIN=K12;
RX PubMed=1460056; DOI=10.1016/s0021-9258(19)74084-8;
RA Huang S., Deutscher M.P.;
RT "Sequence and transcriptional analysis of the Escherichia coli rnt gene
RT encoding RNase T.";
RL J. Biol. Chem. 267:25609-25613(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP CHARACTERIZATION.
RC STRAIN=CA265;
RX PubMed=1704882; DOI=10.1128/jb.173.4.1376-1381.1991;
RA Padmanabha K.P., Deutscher M.P.;
RT "RNase T affects Escherichia coli growth and recovery from metabolic
RT stress.";
RL J. Bacteriol. 173:1376-1381(1991).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF ARG-13; ARG-15;
RP ASP-23; GLU-25; LYS-108; ARG-114; LYS-139; ASP-150; HIS-181 AND ASP-186.
RX PubMed=12364334; DOI=10.1074/jbc.m207706200;
RA Zuo Y., Deutscher M.P.;
RT "Mechanism of action of RNase T. I. Identification of residues required for
RT catalysis, substrate binding, and dimerization.";
RL J. Biol. Chem. 277:50155-50159(2002).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS), CATALYTIC ACTIVITY, FUNCTION,
RP COFACTOR, AND SUBUNIT.
RX PubMed=17437714; DOI=10.1016/j.str.2007.02.004;
RA Zuo Y., Zheng H., Wang Y., Chruszcz M., Cymborowski M., Skarina T.,
RA Savchenko A., Malhotra A., Minor W.;
RT "Crystal structure of RNase T, an exoribonuclease involved in tRNA
RT maturation and end turnover.";
RL Structure 15:417-428(2007).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND DNA
RP AS SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, SITE,
RP COFACTOR, DISRUPTION PHENOTYPE, MUTAGENESIS OF PHE-29; GLU-73; PHE-77;
RP PHE-124 AND PHE-146, AND SUBUNIT.
RX PubMed=21317904; DOI=10.1038/nchembio.524;
RA Hsiao Y.Y., Yang C.C., Lin C.L., Lin J.L., Duh Y., Yuan H.S.;
RT "Structural basis for RNA trimming by RNase T in stable RNA 3'-end
RT maturation.";
RL Nat. Chem. Biol. 7:236-243(2011).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND DNA
RP AS SUBSTRATE ANALOG, COFACTOR, ACTIVE SITE, AND CATALYTIC ACTIVITY.
RX PubMed=22718982; DOI=10.1093/nar/gks548;
RA Hsiao Y.Y., Duh Y., Chen Y.P., Wang Y.T., Yuan H.S.;
RT "How an exonuclease decides where to stop in trimming of nucleic acids:
RT crystal structures of RNase T-product complexes.";
RL Nucleic Acids Res. 40:8144-8154(2012).
CC -!- FUNCTION: Trims short 3' overhangs of a variety of RNA species, leaving
CC a one or two nucleotide 3' overhang. Responsible for the end-turnover
CC of tRNA: specifically removes the terminal AMP residue from uncharged
CC tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis,
CC especially in strains lacking other exoribonucleases.
CC {ECO:0000255|HAMAP-Rule:MF_00157, ECO:0000269|PubMed:12364334,
CC ECO:0000269|PubMed:17437714, ECO:0000269|PubMed:21317904}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00157,
CC ECO:0000269|PubMed:12364334, ECO:0000269|PubMed:17437714,
CC ECO:0000269|PubMed:21317904, ECO:0000269|PubMed:22718982};
CC Note=Binds two Mg(2+) per subunit. The active form of the enzyme binds
CC two Mg(2+) ions in its active site. The first Mg(2+) forms only one
CC salt bridge with the protein. {ECO:0000255|HAMAP-Rule:MF_00157,
CC ECO:0000269|PubMed:12364334, ECO:0000269|PubMed:17437714,
CC ECO:0000269|PubMed:21317904, ECO:0000269|PubMed:22718982};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00157,
CC ECO:0000269|PubMed:17437714, ECO:0000269|PubMed:21317904}.
CC -!- INTERACTION:
CC P30014; P06959: aceF; NbExp=2; IntAct=EBI-557418, EBI-542707;
CC P30014; P30014: rnt; NbExp=3; IntAct=EBI-557418, EBI-557418;
CC -!- DISRUPTION PHENOTYPE: Required for optimal growth.
CC {ECO:0000269|PubMed:21317904}.
CC -!- MISCELLANEOUS: Member of the DEDD group of RNAses that are
CC characterized by the presence of four acidic residues in the active
CC site. These residues are conserved even when the proteins have highly
CC divergent sequences.
CC -!- SIMILARITY: Belongs to the RNase T family. {ECO:0000255|HAMAP-
CC Rule:MF_00157}.
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DR EMBL; L01622; AAC37008.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74724.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15418.2; -; Genomic_DNA.
DR PIR; A45065; A45065.
DR RefSeq; NP_416169.1; NC_000913.3.
DR RefSeq; WP_001282283.1; NZ_SSZK01000001.1.
DR PDB; 2IS3; X-ray; 3.10 A; A/B/C/D=1-215.
DR PDB; 3NGY; X-ray; 2.20 A; A/B/C/D=1-215.
DR PDB; 3NGZ; X-ray; 2.10 A; A/B=1-215.
DR PDB; 3NH0; X-ray; 2.30 A; A/B=1-215.
DR PDB; 3NH1; X-ray; 2.11 A; A/B/C/D=1-215.
DR PDB; 3NH2; X-ray; 2.30 A; A/B/E/F=1-215.
DR PDB; 3V9S; X-ray; 2.10 A; A/B=1-215.
DR PDB; 3V9U; X-ray; 2.30 A; A/B/C/D=1-215.
DR PDB; 3V9W; X-ray; 1.70 A; A/B/C/D=1-215.
DR PDB; 3V9X; X-ray; 1.90 A; A/B/C/D=1-215.
DR PDB; 3V9Z; X-ray; 1.80 A; A/B=1-215.
DR PDB; 3VA0; X-ray; 2.20 A; A/B=1-215.
DR PDB; 3VA3; X-ray; 2.71 A; A/B=1-215.
DR PDB; 4KAZ; X-ray; 1.90 A; A=1-215.
DR PDB; 4KB0; X-ray; 2.00 A; A/B=1-215.
DR PDB; 4KB1; X-ray; 1.80 A; A/B=1-215.
DR PDBsum; 2IS3; -.
DR PDBsum; 3NGY; -.
DR PDBsum; 3NGZ; -.
DR PDBsum; 3NH0; -.
DR PDBsum; 3NH1; -.
DR PDBsum; 3NH2; -.
DR PDBsum; 3V9S; -.
DR PDBsum; 3V9U; -.
DR PDBsum; 3V9W; -.
DR PDBsum; 3V9X; -.
DR PDBsum; 3V9Z; -.
DR PDBsum; 3VA0; -.
DR PDBsum; 3VA3; -.
DR PDBsum; 4KAZ; -.
DR PDBsum; 4KB0; -.
DR PDBsum; 4KB1; -.
DR AlphaFoldDB; P30014; -.
DR SMR; P30014; -.
DR BioGRID; 4260267; 149.
DR BioGRID; 850519; 1.
DR DIP; DIP-10734N; -.
DR IntAct; P30014; 2.
DR STRING; 511145.b1652; -.
DR ChEMBL; CHEMBL3879866; -.
DR jPOST; P30014; -.
DR PaxDb; P30014; -.
DR PRIDE; P30014; -.
DR EnsemblBacteria; AAC74724; AAC74724; b1652.
DR EnsemblBacteria; BAA15418; BAA15418; BAA15418.
DR GeneID; 946159; -.
DR KEGG; ecj:JW1644; -.
DR KEGG; eco:b1652; -.
DR PATRIC; fig|1411691.4.peg.607; -.
DR EchoBASE; EB1509; -.
DR eggNOG; COG0847; Bacteria.
DR HOGENOM; CLU_082724_0_0_6; -.
DR InParanoid; P30014; -.
DR OMA; CYMVNHL; -.
DR PhylomeDB; P30014; -.
DR BioCyc; EcoCyc:EG11547-MON; -.
DR BioCyc; MetaCyc:EG11547-MON; -.
DR BRENDA; 3.1.13.3; 2026.
DR EvolutionaryTrace; P30014; -.
DR PRO; PR:P30014; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:EcoCyc.
DR GO; GO:0016896; F:exoribonuclease activity, producing 5'-phosphomonoesters; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0045004; P:DNA replication proofreading; IBA:GO_Central.
DR GO; GO:0042780; P:tRNA 3'-end processing; IBA:GO_Central.
DR CDD; cd06134; RNaseT; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR HAMAP; MF_00157; RNase_T; 1.
DR InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
DR InterPro; IPR005987; RNase_T.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR PANTHER; PTHR30231:SF2; PTHR30231:SF2; 1.
DR Pfam; PF00929; RNase_T; 1.
DR SMART; SM00479; EXOIII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR TIGRFAMs; TIGR01298; RNaseT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome; tRNA processing.
FT CHAIN 1..215
FT /note="Ribonuclease T"
FT /id="PRO_0000208960"
FT DOMAIN 20..194
FT /note="Exonuclease"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00157"
FT ACT_SITE 181
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00157,
FT ECO:0000269|PubMed:21317904, ECO:0000269|PubMed:22718982"
FT BINDING 23
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT BINDING 23
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 25
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT BINDING 186
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT SITE 29
FT /note="Important for substrate binding and specificity"
FT SITE 73
FT /note="Important for substrate binding and specificity"
FT SITE 77
FT /note="Important for substrate binding and specificity"
FT SITE 124
FT /note="Important for substrate binding and specificity"
FT SITE 146
FT /note="Important for substrate binding and specificity"
FT MUTAGEN 13
FT /note="R->A: Strongly reduces affinity for RNA. Nearly
FT abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 15
FT /note="R->A: Strongly reduces affinity for RNA."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 23
FT /note="D->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 25
FT /note="E->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 29
FT /note="F->A: Abolishes enzyme activity; when associated
FT with A-73 and A-77."
FT /evidence="ECO:0000269|PubMed:21317904"
FT MUTAGEN 73
FT /note="E->A: Reduces enzyme activity. Abolishes enzyme
FT activity; when associated with A-29 and A-77."
FT /evidence="ECO:0000269|PubMed:21317904"
FT MUTAGEN 77
FT /note="F->A: Abolishes enzyme activity; when associated
FT with A-29 and A-73."
FT /evidence="ECO:0000269|PubMed:21317904"
FT MUTAGEN 108
FT /note="K->A: Strongly reduces affinity for RNA."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 114
FT /note="R->A: Strongly reduces affinity for RNA."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 124
FT /note="F->A: Abolishes enzyme activity; when associated
FT with A-146."
FT /evidence="ECO:0000269|PubMed:21317904"
FT MUTAGEN 139
FT /note="K->A: Reduces affinity for RNA."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 146
FT /note="F->A: Abolishes enzyme activity; when associated
FT with A-124."
FT /evidence="ECO:0000269|PubMed:21317904"
FT MUTAGEN 150
FT /note="D->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 181
FT /note="H->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT MUTAGEN 186
FT /note="D->A: Nearly abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:12364334"
FT HELIX 5..7
FT /evidence="ECO:0007829|PDB:3NH1"
FT HELIX 10..13
FT /evidence="ECO:0007829|PDB:3V9W"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:3V9W"
FT STRAND 17..29
FT /evidence="ECO:0007829|PDB:3V9W"
FT TURN 31..33
FT /evidence="ECO:0007829|PDB:3V9W"
FT STRAND 36..46
FT /evidence="ECO:0007829|PDB:3V9W"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:3NGY"
FT STRAND 52..62
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 72..78
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 92..107
FT /evidence="ECO:0007829|PDB:3V9W"
FT TURN 108..111
FT /evidence="ECO:0007829|PDB:3V9W"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:3V9W"
FT TURN 120..122
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 123..135
FT /evidence="ECO:0007829|PDB:3V9W"
FT STRAND 143..150
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 151..159
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 164..171
FT /evidence="ECO:0007829|PDB:3V9W"
FT TURN 177..181
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 183..203
FT /evidence="ECO:0007829|PDB:3V9W"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:3V9Z"
SQ SEQUENCE 215 AA; 23523 MW; 502C1CCEFABF4B05 CRC64;
MSDNAQLTGL CDRFRGFYPV VIDVETAGFN AKTDALLEIA AITLKMDEQG WLMPDTTLHF
HVEPFVGANL QPEALAFNGI DPNDPDRGAV SEYEALHEIF KVVRKGIKAS GCNRAIMVAH
NANFDHSFMM AAAERASLKR NPFHPFATFD TAALAGLALG QTVLSKACQT AGMDFDSTQA
HSALYDTERT AVLFCEIVNR WKRLGGWPLS AAEEV
