RNPH_ECOBW
ID RNPH_ECOBW Reviewed; 238 AA.
AC P0CG18; A8DYQ0; C4ZXN5; P03842;
DT 15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
DT 15-JUN-2010, sequence version 1.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=Ribonuclease PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE Short=RNase PH {ECO:0000255|HAMAP-Rule:MF_00564};
DE EC=2.7.7.56 {ECO:0000255|HAMAP-Rule:MF_00564, ECO:0000269|PubMed:1512253};
DE AltName: Full=tRNA nucleotidyltransferase {ECO:0000255|HAMAP-Rule:MF_00564};
GN Name=rph {ECO:0000255|HAMAP-Rule:MF_00564, ECO:0000303|PubMed:1885537};
GN Synonyms=orfE {ECO:0000303|PubMed:1885537}; OrderedLocusNames=BWG_3334;
OS Escherichia coli (strain K12 / MC4100 / BW2952).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=595496;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=6207018; DOI=10.1002/j.1460-2075.1984.tb02046.x;
RA Poulsen P., Bonekamp F., Jensen K.F.;
RT "Structure of the Escherichia coli pyrE operon and control of pyrE
RT expression by a UTP modulated intercistronic attentuation.";
RL EMBO J. 3:1783-1790(1984).
RN [2]
RP FUNCTION, SUBUNIT, AND PROTEIN SEQUENCE OF 1-21.
RC STRAIN=K12 / CA265 / 18-11;
RX PubMed=1885537; DOI=10.1128/jb.173.17.5589-5591.1991;
RA Ost K.A., Deutscher M.P.;
RT "Escherichia coli orfE (upstream of pyrE) encodes RNase PH.";
RL J. Bacteriol. 173:5589-5591(1991).
RN [3]
RP IMPORTANCE AT HIGH TEMPERATURE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=1925027; DOI=10.1016/0923-2508(91)90042-9;
RA Poulsen P., Jensen K.F.;
RT "Three genes preceding pyrE on the Escherichia coli chromosome are
RT essential for survival and normal cell morphology in stationary culture and
RT at high temperature.";
RL Res. Microbiol. 142:283-288(1991).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=K12 / MC1000 / ATCC 39531;
RX PubMed=1512252; DOI=10.1016/s0021-9258(18)41906-0;
RA Jensen K.F., Andersen J.T., Poulsen P.;
RT "Overexpression and rapid purification of the orfE/rph gene product, RNase
RT PH of Escherichia coli.";
RL J. Biol. Chem. 267:17147-17152(1992).
RN [5]
RP CHARACTERIZATION.
RC STRAIN=K12 / MC1000 / ATCC 39531;
RX PubMed=1512253; DOI=10.1016/s0021-9258(18)41907-2;
RA Kelly K.O., Deutscher M.P.;
RT "Characterization of Escherichia coli RNase PH.";
RL J. Biol. Chem. 267:17153-17158(1992).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MC4100 / BW2952;
RX PubMed=19376874; DOI=10.1128/jb.00118-09;
RA Ferenci T., Zhou Z., Betteridge T., Ren Y., Liu Y., Feng L., Reeves P.R.,
RA Wang L.;
RT "Genomic sequencing reveals regulatory mutations and recombinational events
RT in the widely used MC4100 lineage of Escherichia coli K-12.";
RL J. Bacteriol. 191:4025-4029(2009).
CC -!- FUNCTION: Phosphorolytic exoribonuclease that plays an important role
CC in tRNA 3'-end maturation; has no activity on a tRNA precursor with a
CC 3'-terminal phosphate group (PubMed:1512253). In vitro is freely
CC reversible, adds nucleotides to the ends of RNA molecules by using
CC nucleoside diphosphates as substrates, but this may not be
CC physiologically important (PubMed:1512253). Probably plays a role in
CC initiation of 16S rRNA degradation (leading to ribosome degradation)
CC during starvation. {ECO:0000269|PubMed:1512253,
CC ECO:0000269|PubMed:1885537}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate +
CC tRNA(n); Xref=Rhea:RHEA:10628, Rhea:RHEA-COMP:17343, Rhea:RHEA-
CC COMP:17344, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:173114;
CC EC=2.7.7.56; Evidence={ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000269|PubMed:1512253};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:1512253};
CC Note=Can also use Mn(2+) or Co(2+) with reduced efficiency. K(+)
CC simulates the degradative reaction. {ECO:0000269|PubMed:1512253};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2 mM for phosphate in the degradative reaction
CC {ECO:0000269|PubMed:1512253};
CC KM=1 uM for tRNA-CCA-C2-3 in the degradative reaction
CC {ECO:0000269|PubMed:1512253};
CC pH dependence:
CC Optimum pH is 8-9 for degradation (PubMed:1512253).
CC {ECO:0000269|PubMed:1512253};
CC Temperature dependence:
CC Optimum temperature is 40 degrees Celsius activity drops off quickly
CC from 45 degrees Celsius (PubMed:1512253).
CC {ECO:0000269|PubMed:1512253};
CC -!- SUBUNIT: Homodimer (PubMed:1885537). Has a tendency to aggregate into
CC multimers (PubMed:1512253). {ECO:0000269|PubMed:1512253,
CC ECO:0000305|PubMed:1885537}.
CC -!- MISCELLANEOUS: The gene in K12 strains MG1655 and W3110 (and also other
CC derivatives of K12 W1485) has a frameshift mutation that leads to loss
CC of activity, although the protein may be translated. Thus in those
CC strains rph is an expressed catalytically inactive protein. Strains
CC shown in this entry are derivatives of K12 MC1000 or MC4100, in which
CC the frameshift has not occured and thus are active.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; X00781; CAA25357.1; -; Genomic_DNA.
DR EMBL; CP001396; ACR62740.1; -; Genomic_DNA.
DR RefSeq; WP_001247096.1; NC_012759.1.
DR AlphaFoldDB; P0CG18; -.
DR SMR; P0CG18; -.
DR KEGG; ebw:BWG_3334; -.
DR HOGENOM; CLU_050858_0_0_6; -.
DR OMA; KGKGQGW; -.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016075; P:rRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR CDD; cd11362; RNase_PH_bact; 1.
DR Gene3D; 3.30.230.70; -; 1.
DR HAMAP; MF_00564; RNase_PH; 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; IPR002381; RNase_PH_bac-type.
DR InterPro; IPR018336; RNase_PH_CS.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
DR TIGRFAMs; TIGR01966; RNasePH; 1.
DR PROSITE; PS01277; RIBONUCLEASE_PH; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Nucleotidyltransferase; RNA-binding;
KW rRNA processing; Transferase; tRNA processing; tRNA-binding.
FT CHAIN 1..238
FT /note="Ribonuclease PH"
FT /id="PRO_1000212061"
FT BINDING 86
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT BINDING 124..126
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00564"
FT CONFLICT 123..124
FT /note="GG -> AW (in Ref. 1; CAA25357)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 238 AA; 25352 MW; 7299C5C8F2364D34 CRC64;
MRPAGRSNNQ VRPVTLTRNY TKHAEGSVLV EFGDTKVLCT ASIEEGVPRF LKGQGQGWIT
AEYGMLPRST HTRNAREAAK GKQGGRTMEI QRLIARALRA AVDLKALGEF TITLDCDVLQ
ADGGTRTASI TGACVALVDA LQKLVENGKL KTNPMKGMVA AVSVGIVNGE AVCDLEYVED
SAAETDMNVV MTEDGRIIEV QGTAEGEPFT HEELLILLAL ARGGIESIVA TQKAALAN
