RNPH_ECOLI
ID RNPH_ECOLI Reviewed; 228 AA.
AC P0CG19; A0A385XJN7; A8DYQ0; P03842;
DT 15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
DT 15-JUN-2010, sequence version 1.
DT 03-AUG-2022, entry version 64.
DE RecName: Full=Truncated inactive ribonuclease PH;
DE Short=Truncated inactive RNase PH;
DE AltName: Full=Inactive RNase PH {ECO:0000305|PubMed:8501045};
DE AltName: Full=Truncated RNase PH {ECO:0000303|PubMed:8501045};
GN Name=rph {ECO:0000255|HAMAP-Rule:MF_00564, ECO:0000303|PubMed:8501045};
GN Synonyms=orfE; OrderedLocusNames=b3643, JW3618;
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 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 208-228 (STRAIN W3110), EXPRESSION,
RP AND LOSS OF ACTIVITY IN SOME K12 STRAINS.
RC STRAIN=K12 / ATCC 12435 / DSM 5695 / NBRC 3302 / NCIMB 9481 / W1485,
RC K12 / MG1655 / ATCC 47076, and K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8501045; DOI=10.1128/jb.175.11.3401-3407.1993;
RA Jensen K.F.;
RT "The Escherichia coli K-12 'wild types' W3110 and MG1655 have an rph
RT frameshift mutation that leads to pyrimidine starvation due to low pyrE
RT expression levels.";
RL J. Bacteriol. 175:3401-3407(1993).
RN [5]
RP FUNCTION IN RIBOSOME DEGRADATION DURING STARVATION.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=21135037; DOI=10.1261/rna.2448911;
RA Basturea G.N., Zundel M.A., Deutscher M.P.;
RT "Degradation of ribosomal RNA during starvation: comparison to quality
RT control during steady-state growth and a role for RNase PH.";
RL RNA 17:338-345(2011).
RN [6]
RP FUNCTION IN RRNA DEGRADATION.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=27298395; DOI=10.1261/rna.056275.116;
RA Sulthana S., Basturea G.N., Deutscher M.P.;
RT "Elucidation of pathways of ribosomal RNA degradation: an essential role
RT for RNase E.";
RL RNA 22:1163-1171(2016).
RN [7]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=28625967; DOI=10.1261/rna.060558.116;
RA Sulthana S., Quesada E., Deutscher M.P.;
RT "RNase II regulates RNase PH and is essential for cell survival during
RT starvation and stationary phase.";
RL RNA 23:1456-1464(2017).
RN [8]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / MG1693;
RX PubMed=28808133; DOI=10.1128/jb.00301-17;
RA Bowden K.E., Wiese N.S., Perwez T., Mohanty B.K., Kushner S.R.;
RT "The rph-1-encoded truncated RNase PH protein inhibits RNase P maturation
RT of pre-tRNAs with short leader sequences in the absence of RppH.";
RL J. Bacteriol. 199:0-0(2017).
CC -!- FUNCTION: This an expressed but non-active exoribonuclease allele
CC (PubMed:8501045). The catalytically inactive protein translated in
CC strain K12 MG1655 inhibits the 5'-processing of primary pre-tRNAs with
CC short (<5 nucleotide) leaders in a dominant-negative effect when RNA
CC pyrophosphohydrolase (rppH) is also inactive; perhaps inactive Rph
CC inhibits interaction with RNase P which is exacerbated when RppH cannot
CC cleave the triphosphate of the primary transcript (PubMed:28808133).
CC {ECO:0000269|PubMed:28808133, ECO:0000269|PubMed:8501045}.
CC -!- SUBUNIT: Homodimer (By similarity). No interaction between the inactive
CC protein and RppH or RNase P was detected by immunoprecipitation
CC (PubMed:28808133). {ECO:0000255|HAMAP-Rule:MF_00564,
CC ECO:0000305|PubMed:28808133}.
CC -!- INDUCTION: The catalytically inactive protein is present at
CC significantly lower levels than restored wild-type protein (at protein
CC level) (PubMed:28808133). {ECO:0000269|PubMed:28808133}.
CC -!- DISRUPTION PHENOTYPE: When the gene is deleted the strain no longer
CC inhibits 5'-processing of pre-tRNAs with short (<5 nucleotide) leaders
CC in the absence of rppH (PubMed:28808133). The truncated allele encoded
CC by this protein has a slight growth defect, which is slightly
CC exacerbated when combined with an rppH deletion (PubMed:28808133). The
CC truncated allele suppresses the loss of viability conferred by deletion
CC of RNase 2 (rnb) during stationary phase at 31 and 42 degrees Celsius
CC or starvation at 42 degrees Celsius (PubMed:28625967).
CC {ECO:0000269|PubMed:28625967, ECO:0000269|PubMed:28808133}.
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 is translated. Thus in those strains
CC rph is an expressed, catalytically inactive protein (PubMed:8501045).
CC In strain K12 / MG1655(Seq)* the wild-type protein has been restored
CC (PubMed:21135037, PubMed:27298395, PubMed:28625967). For the functional
CC protein without the frameshift mutation see AC P0CG18.
CC {ECO:0000269|PubMed:21135037, ECO:0000269|PubMed:27298395,
CC ECO:0000269|PubMed:28625967, ECO:0000269|PubMed:8501045}.
CC -!- MISCELLANEOUS: The (restored) wild-type protein plays a significant
CC role in tRNA 3'-end maturation when a C nucleotide follows the mature
CC CCA terminus (PubMed:28808133). Wild-type (restored) protein also plays
CC a critical role in initiating 16S rRNA degradation (leading to ribosome
CC degradation) during starvation, but not in rRNA quality control during
CC steady state growth (PubMed:21135037, PubMed:27298395). The wild-type
CC (restored) protein is rapidly turned over at 42 degrees Celsius during
CC starvation, but not at 31 degrees Celsius with or without starvation;
CC in the absence of RNase 2 (rnb) protein levels do not decline (at
CC protein level) (PubMed:28625967). {ECO:0000269|PubMed:21135037,
CC ECO:0000269|PubMed:27298395, ECO:0000269|PubMed:28625967,
CC ECO:0000269|PubMed:28808133}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
CC Rule:MF_00564}.
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DR EMBL; V01578; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; L10328; AAA61996.1; -; Genomic_DNA.
DR EMBL; U00096; AYC08250.1; -; Genomic_DNA.
DR EMBL; AP009048; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; X72920; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A04470; QQECPE.
DR AlphaFoldDB; P0CG19; -.
DR SMR; P0CG19; -.
DR DIP; DIP-10738N; -.
DR IntAct; P0CG19; 9.
DR PaxDb; P0CG19; -.
DR PRIDE; P0CG19; -.
DR EnsemblBacteria; AYC08250; AYC08250; b3643.
DR InParanoid; P0CG19; -.
DR PhylomeDB; P0CG19; -.
DR BioCyc; EcoCyc:EG10863-MON; -.
DR BRENDA; 2.7.7.56; 2026.
DR PRO; PR:P0CG19; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IDA:EcoCyc.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
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 Reference proteome; RNA-binding; rRNA processing; tRNA processing;
KW tRNA-binding.
FT CHAIN 1..228
FT /note="Truncated inactive ribonuclease PH"
FT /id="PRO_0000139889"
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"
SQ SEQUENCE 228 AA; 24425 MW; 028BC8F5A6859447 CRC64;
MRPAGRSNNQ VRPVTLTRNY TKHAEGSVLV EFGDTKVLCT ASIEEGVPRF LKGQGQGWIT
AEYGMLPRST HTRNAREAAK GKQGGRTMEI QRLIARALRA AVDLKALGEF TITLDCDVLQ
ADGGTRTASI TGACVALVDA LQKLVENGKL KTNPMKGMVA AVSVGIVNGE AVCDLEYVED
SAAETDMNVV MTEDGRIIEV QGTAEGEPFT HEELLILLAL ARGESNPL
