RNM_ECOLI
ID RNM_ECOLI Reviewed; 293 AA.
AC P77766;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=5'-3' exoribonuclease Rnm {ECO:0000305};
DE EC=3.1.13.- {ECO:0000269|PubMed:25871919, ECO:0000269|PubMed:32343306};
DE AltName: Full=3',5'-nucleotide bisphosphate phosphatase {ECO:0000305|PubMed:25871919};
DE EC=3.1.3.97 {ECO:0000269|PubMed:25871919};
DE AltName: Full=RNase AM {ECO:0000303|PubMed:25871919};
GN Name=rnm {ECO:0000305}; Synonyms=trpH {ECO:0000250|UniProtKB:O54453}, yciV;
GN OrderedLocusNames=b1266 {ECO:0000312|EMBL:AAC74348.1},
GN JW1258 {ECO:0000312|EMBL:BAA14800.1};
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=25871919; DOI=10.1021/acs.biochem.5b00192;
RA Ghodge S.V., Raushel F.M.;
RT "Discovery of a previously unrecognized ribonuclease from Escherichia coli
RT that hydrolyzes 5'-phosphorylated fragments of RNA.";
RL Biochemistry 54:2911-2918(2015).
RN [5]
RP FUNCTION IN RRNA PROCESSING, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=32343306; DOI=10.1093/nar/gkaa260;
RA Jain C.;
RT "RNase AM, a 5' to 3' exonuclease, matures the 5' end of all three
RT ribosomal RNAs in E. coli.";
RL Nucleic Acids Res. 48:5616-5623(2020).
CC -!- FUNCTION: Exoribonuclease that catalyzes the last steps of 5S, 16S and
CC 23S rRNA 5'-end maturation. Removes 3 nucleotides (nt) from the 5' end
CC of 5S, 16S and 23S rRNA precursors to generate the mature 5' ends.
CC Precursors with longer extensions are not processed (7 nt at the 5' end
CC of pre-23S rRNA or 66 nt at the 5'-end of 16S rRNA are not processed).
CC 5S and 23S rRNA maturation occurs more efficiently and accurately on
CC ribosomal particles as compared to free RNA; the enzyme overdigests
CC free RNA but generates the correct 5'-end in ribosomes from rnm
CC deletion strains (PubMed:32343306). Efficiently catalyzes the
CC hydrolysis of the 3'-phosphate from 3',5'-bis-phosphonucleotides as
CC well as the successive hydrolysis of 5'-phosphomononucleotides from the
CC 5'-end of short pieces of RNA and DNA, with no specificity toward the
CC identity of the nucleotide base. Is more efficient at hydrolyzing RNA
CC oligonucleotides than DNA oligonucleotides. This enzyme can also
CC hydrolyze annealed DNA duplexes, albeit at a catalytic efficiency
CC approximately 10-fold lower than that of the corresponding single-
CC stranded oligonucleotides. {ECO:0000269|PubMed:25871919,
CC ECO:0000269|PubMed:32343306}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 3',5'-bisphosphate + H2O = a ribonucleoside
CC 5'-phosphate + phosphate; Xref=Rhea:RHEA:43532, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58043, ChEBI:CHEBI:83402; EC=3.1.3.97;
CC Evidence={ECO:0000269|PubMed:25871919};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:25871919};
CC Note=Binds 1 Mn(2+) ion per subunit (PubMed:25871919). However, the
CC sequence similarity to CV_1693 from C.violaceum tends to indicate a
CC trinuclear metal center. {ECO:0000269|PubMed:25871919, ECO:0000305};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=56 uM for pAp {ECO:0000269|PubMed:25871919};
CC KM=53 uM for 2'-deoxy-pAp {ECO:0000269|PubMed:25871919};
CC KM=86 uM for pCp (2'5'/3'5' mixture) {ECO:0000269|PubMed:25871919};
CC KM=114 uM for 2'-deoxy-pCp {ECO:0000269|PubMed:25871919};
CC KM=45 uM for pGp (2'5'/3'5' mixture) {ECO:0000269|PubMed:25871919};
CC KM=30 uM for 2'-deoxy-pGp {ECO:0000269|PubMed:25871919};
CC KM=59 uM for pUp (2'5'/3'5' mixture) {ECO:0000269|PubMed:25871919};
CC KM=110 uM for 2'-deoxy-pUp {ECO:0000269|PubMed:25871919};
CC KM=32 uM for 2'-deoxy-pTp {ECO:0000269|PubMed:25871919};
CC KM=48 uM for 2'-deoxy-pIp {ECO:0000269|PubMed:25871919};
CC KM=420 uM for 3'-AMP {ECO:0000269|PubMed:25871919};
CC KM=14.0 uM for p(Gp)G {ECO:0000269|PubMed:25871919};
CC KM=160 uM for p(Ap)A {ECO:0000269|PubMed:25871919};
CC KM=55 uM for p(Ap)(2)A {ECO:0000269|PubMed:25871919};
CC KM=45 uM for p(Ap)(3)A {ECO:0000269|PubMed:25871919};
CC KM=59 uM for p(Ap)(4)A {ECO:0000269|PubMed:25871919};
CC KM=149 uM for p(dAp)dA {ECO:0000269|PubMed:25871919};
CC KM=67 uM for p(dAp)(2)dA {ECO:0000269|PubMed:25871919};
CC KM=180 uM for p(dAp)(3)dA {ECO:0000269|PubMed:25871919};
CC KM=280 uM for p(dAp)(4)dA {ECO:0000269|PubMed:25871919};
CC Note=kcat is 9.9 sec(-1) with pAp as substrate. kcat is 5.6 sec(-1)
CC with 2'-deoxy-pAp as substrate. kcat is 6.0 sec(-1) with pCp
CC (2'5'/3'5' mixture) as substrate. kcat is 1.9 sec(-1) with 2'-deoxy-
CC pCp as substrate. kcat is 5.5 sec(-1) with pGp (2'5'/3'5' mixture) as
CC substrate. kcat is 1.7 sec(-1) with 2'-deoxy-pGp as substrate. kcat
CC is 4.7 sec(-1) with pUp as substrate. kcat is 2.1 sec(-1) with 2'-
CC deoxy-pUp as substrate. kcat is 1.6 sec(-1) with 2'-deoxy-pTp as
CC substrate. kcat is 3.3 sec(-1) with 2'-deoxy-pIp as substrate. kcat
CC is 0.22 sec(-1) with 3'-AMP as substrate. kcat is 0.60 sec(-1) with
CC p(Gp)G as substrate. kcat is 14 sec(-1) with p(Ap)A as substrate.
CC kcat is 3.8 sec(-1) with p(Ap)(2)A as substrate. kcat is 3.6 sec(-1)
CC with p(Ap)(3)A as substrate. kcat is 2.7 sec(-1) with p(Ap)(4)A as
CC substrate. kcat is 2.5 sec(-1) with p(dAp)dA as substrate. kcat is
CC 0.72 sec(-1) with p(dAp)(2)dA as substrate. kcat is 1.20 sec(-1) with
CC p(dAp)(3)dA as substrate. kcat is 0.79 sec(-1) with p(dAp)(4)dA as
CC substrate. {ECO:0000269|PubMed:25871919};
CC -!- DISRUPTION PHENOTYPE: None of the 3 rRNAs are correctly processed at
CC their 5' ends, each accumulates a precursor with 3 extra nucleotides.
CC {ECO:0000269|PubMed:32343306}.
CC -!- MISCELLANEOUS: Since E.coli possesses another enzyme, CysQ, which has
CC been demonstrated to catalyze the hydrolysis of 3',5'-pAp to 5'-AMP and
CC phosphate during sulfur assimilation, it seems therefore unlikely that
CC the hydrolysis of 3',5'-bis-phosphonucleotides will be the primary
CC physiological function of YciV. {ECO:0000305|PubMed:25871919}.
CC -!- MISCELLANEOUS: Was originally suggested to be involved in tryptophan
CC metabolism, thus the gene synonym trpH. {ECO:0000303|PubMed:9278503}.
CC -!- SIMILARITY: Belongs to the PHP family. TrpH/YciV subfamily.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC74348.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14800.1; -; Genomic_DNA.
DR PIR; E64874; E64874.
DR RefSeq; NP_415782.1; NC_000913.3.
DR RefSeq; WP_001285661.1; NZ_STEB01000005.1.
DR AlphaFoldDB; P77766; -.
DR SMR; P77766; -.
DR BioGRID; 4260125; 43.
DR BioGRID; 850224; 1.
DR IntAct; P77766; 9.
DR STRING; 511145.b1266; -.
DR PaxDb; P77766; -.
DR PRIDE; P77766; -.
DR EnsemblBacteria; AAC74348; AAC74348; b1266.
DR EnsemblBacteria; BAA14800; BAA14800; BAA14800.
DR GeneID; 66674911; -.
DR GeneID; 945857; -.
DR KEGG; ecj:JW1258; -.
DR KEGG; eco:b1266; -.
DR PATRIC; fig|511145.12.peg.1315; -.
DR EchoBASE; EB4005; -.
DR eggNOG; COG0613; Bacteria.
DR HOGENOM; CLU_067347_0_0_6; -.
DR InParanoid; P77766; -.
DR OMA; CTWGGAT; -.
DR PhylomeDB; P77766; -.
DR BioCyc; EcoCyc:G6634-MON; -.
DR BioCyc; MetaCyc:G6634-MON; -.
DR PRO; PR:P77766; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0097657; F:3',5'-nucleotide bisphosphate phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0035312; F:5'-3' exodeoxyribonuclease activity; IDA:EcoCyc.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0008252; F:nucleotidase activity; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0000481; P:maturation of 5S rRNA; IDA:EcoCyc.
DR GO; GO:0000470; P:maturation of LSU-rRNA; IDA:EcoCyc.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IDA:EcoCyc.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR003141; Pol/His_phosphatase_N.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR Pfam; PF02811; PHP; 1.
DR SMART; SM00481; POLIIIAc; 1.
DR SUPFAM; SSF89550; SSF89550; 1.
PE 1: Evidence at protein level;
KW Exonuclease; Hydrolase; Manganese; Metal-binding; Nuclease;
KW Nucleotide-binding; Reference proteome; rRNA processing.
FT CHAIN 1..293
FT /note="5'-3' exoribonuclease Rnm"
FT /id="PRO_0000065638"
FT BINDING 13
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 15
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 20
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 45
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 72
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 72
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 83
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 198
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 255
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
FT BINDING 257
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q7NXD4"
SQ SEQUENCE 293 AA; 32580 MW; 0A045925C472A15F CRC64;
MSDTNYAVIY DLHSHTTASD GCLTPEALVH RAVEMRVGTL AITDHDTTAA IAPAREEISR
SGLALNLIPG VEISTVWENH EIHIVGLNID ITHPLMCEFL AQQTERRNQR AQLIAERLEK
AQIPGALEGA QRLAQGGAVT RGHFARFLVE CGKASSMADV FKKYLARGKT GYVPPQWCTI
EQAIDVIHHS GGKAVLAHPG RYNLSAKWLK RLVAHFAEHH GDAMEVAQCQ QSPNERTQLA
ALARQHHLWA SQGSDFHQPC PWIELGRKLW LPAGVEGVWQ LWEQPQNTTE REL
