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Truncated inactive ribonuclease PH (Truncated inactive RNase PH) (Inactive RNase PH) (Truncated RNase PH)

 RNPH_ECOLI              Reviewed;         228 AA.
P0CG19; A8DYQ0; P03842;
15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
15-JUN-2010, sequence version 1.
23-MAY-2018, entry version 46.
RecName: Full=Truncated inactive ribonuclease PH;
Short=Truncated inactive RNase PH;
AltName: Full=Inactive RNase PH {ECO:0000305|PubMed:8501045};
AltName: Full=Truncated RNase PH {ECO:0000303|PubMed:8501045};
Name=rph {ECO:0000255|HAMAP-Rule:MF_00564}; Synonyms=orfE;
OrderedLocusNames=b3643, JW3618;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7686882; DOI=10.1006/geno.1993.1230;
Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
"DNA sequence and analysis of 136 kilobases of the Escherichia coli
genome: organizational symmetry around the origin of replication.";
Genomics 16:551-561(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 208-228 (STRAIN W3110),
EXPRESSION, AND LOSS OF ACTIVITY IN SOME K12 STRAINS.
STRAIN=K12 / MG1655 / ATCC 47076, K12 / W1485, and
K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8501045; DOI=10.1128/jb.175.11.3401-3407.1993;
Jensen K.F.;
"The Escherichia coli K-12 'wild types' W3110 and MG1655 have an rph
frameshift mutation that leads to pyrimidine starvation due to low
pyrE expression levels.";
J. Bacteriol. 175:3401-3407(1993).
[5]
FUNCTION IN RIBOSOME DEGRADATION DURING STARVATION.
STRAIN=K12 / MG1655(Seq)*;
PubMed=21135037; DOI=10.1261/rna.2448911;
Basturea G.N., Zundel M.A., Deutscher M.P.;
"Degradation of ribosomal RNA during starvation: comparison to quality
control during steady-state growth and a role for RNase PH.";
RNA 17:338-345(2011).
[6]
FUNCTION IN RRNA DEGRADATION.
STRAIN=K12 / MG1655(Seq)*;
PubMed=27298395; DOI=10.1261/rna.056275.116;
Sulthana S., Basturea G.N., Deutscher M.P.;
"Elucidation of pathways of ribosomal RNA degradation: an essential
role for RNase E.";
RNA 22:1163-1171(2016).
[7]
FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / MG1655(Seq)*;
PubMed=28625967; DOI=10.1261/rna.060558.116;
Sulthana S., Quesada E., Deutscher M.P.;
"RNase II regulates RNase PH and is essential for cell survival during
starvation and stationary phase.";
RNA 23:1456-1464(2017).
[8]
FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / MG1655 / MG1693;
PubMed=28808133; DOI=10.1128/JB.00301-17;
Bowden K.E., Wiese N.S., Perwez T., Mohanty B.K., Kushner S.R.;
"The rph-1-encoded truncated RNase PH protein inhibits RNase P
maturation of pre-tRNAs with short leader sequences in the absence of
RppH.";
J. Bacteriol. 199:0-0(2017).
-!- FUNCTION: This an expressed but non-active exoribonuclease allele
(PubMed:8501045). The catalytically inactive protein translated in
strain K12 MG1655 inhibits the 5'-processing of primary pre-tRNAs
with short (<5 nucleotide) leaders in a dominant-negative effect
when RNA pyrophosphohydrolase (rppH) is also inactive; perhaps
inactive Rph inhibits interaction with RNase P which is
exacerbated when RppH cannot cleave the triphosphate of the
primary transcript (PubMed:28808133).
{ECO:0000269|PubMed:28808133, ECO:0000269|PubMed:8501045}.
-!- SUBUNIT: Homodimer (By similarity). No interaction between the
inactive protein and RppH or RNase P was detected by
immunoprecipitation (PubMed:28808133). {ECO:0000255|HAMAP-
Rule:MF_00564, ECO:0000305|PubMed:28808133}.
-!- INDUCTION: The catalytically inactive protein is present at
significantly lower levels than restored wild-type protein (at
protein level) (PubMed:28808133). {ECO:0000269|PubMed:28808133}.
-!- DISRUPTION PHENOTYPE: When the gene is deleted the strain no
longer inhibits 5'-processing of pre-tRNAs with short (<5
nucleotide) leaders in the absence of rppH (PubMed:28808133). The
truncated allele encoded by this protein has a slight growth
defect, which is slightly exacerbated when combined with an rppH
deletion (PubMed:28808133). The truncated allele suppresses the
loss of viability conferred by deletion of RNase 2 (rnb) during
stationary phase at 31 and 42 degrees Celsius or starvation at 42
degrees Celsius (PubMed:28625967). {ECO:0000269|PubMed:28625967,
ECO:0000269|PubMed:28808133}.
-!- MISCELLANEOUS: The gene in K12 strains MG1655 and W3110 (and also
other derivatives of K12 W1485) has a frameshift mutation that
leads to loss of activity, although the protein is translated.
Thus in those strains rph is an expressed, catalytically inactive
protein (PubMed:8501045). In strain K12 / MG1655(Seq)* the wild-
type protein has been restored (PubMed:21135037, PubMed:27298395,
PubMed:28625967). For the functional protein without the
frameshift mutation see AC P0CG18. {ECO:0000269|PubMed:21135037,
ECO:0000269|PubMed:27298395, ECO:0000269|PubMed:28625967,
ECO:0000269|PubMed:8501045}.
-!- MISCELLANEOUS: The (restored) wild-type protein plays a
significant role in tRNA 3'-end maturation when a C nucleotide
follows the mature CCA terminus (PubMed:28808133). Wild-type
(restored) protein also plays a critical role in initiating 16S
rRNA degradation (leading to ribosome degradation) during
starvation, but not in rRNA quality control during steady state
growth (PubMed:21135037, PubMed:27298395). The wild-type
(restored) protein is rapidly turned over at 42 degrees Celsius
during starvation, but not at 31 degrees Celsius with or without
starvation; in the absence of RNase 2 (rnb) protein levels do not
decline (at protein level) (PubMed:28625967).
{ECO:0000269|PubMed:21135037, ECO:0000269|PubMed:27298395,
ECO:0000269|PubMed:28625967, ECO:0000269|PubMed:28808133}.
-!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000255|HAMAP-
Rule:MF_00564}.
-----------------------------------------------------------------------
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EMBL; V01578; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; L10328; AAA61996.1; -; Genomic_DNA.
EMBL; U00096; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AP009048; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; X72920; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; A04470; QQECPE.
ProteinModelPortal; P0CG19; -.
SMR; P0CG19; -.
DIP; DIP-10738N; -.
IntAct; P0CG19; 9.
STRING; 511145.b3643; -.
EPD; P0CG19; -.
PaxDb; P0CG19; -.
PRIDE; P0CG19; -.
EcoGene; EG10863; rph.
eggNOG; ENOG4105ED0; Bacteria.
eggNOG; COG0689; LUCA.
InParanoid; P0CG19; -.
BioCyc; EcoCyc:EG10863-MONOMER; -.
BioCyc; MetaCyc:EG10863-MONOMER; -.
PRO; PR:P0CG19; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:EcoCyc.
GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IDA:EcoCyc.
GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
CDD; cd11362; RNase_PH_bact; 1.
Gene3D; 3.30.230.70; -; 1.
HAMAP; MF_00564; RNase_PH; 1.
InterPro; IPR001247; ExoRNase_PH_dom1.
InterPro; IPR015847; ExoRNase_PH_dom2.
InterPro; IPR036345; ExoRNase_PH_dom2_sf.
InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
InterPro; IPR002381; RNase_PH_bac-type.
InterPro; IPR018336; RNase_PH_CS.
Pfam; PF01138; RNase_PH; 1.
Pfam; PF03725; RNase_PH_C; 1.
SUPFAM; SSF54211; SSF54211; 1.
SUPFAM; SSF55666; SSF55666; 1.
TIGRFAMs; TIGR01966; RNasePH; 1.
PROSITE; PS01277; RIBONUCLEASE_PH; 1.
1: Evidence at protein level;
Complete proteome; Reference proteome; RNA-binding; rRNA processing;
tRNA processing; tRNA-binding.
CHAIN 1 228 Truncated inactive ribonuclease PH.
/FTId=PRO_0000139889.
REGION 124 126 Phosphate (substrate) binding.
{ECO:0000255|HAMAP-Rule:MF_00564}.
BINDING 86 86 Phosphate (substrate) binding.
{ECO:0000255|HAMAP-Rule:MF_00564}.
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


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