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Protein

Truncated inactive ribonuclease PH

Gene

rph

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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).2 Publications

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 P0CG18.4 Publications
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).4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei86Phosphate (substrate) bindingUniRule annotation1

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: EcoCyc
  • tRNA binding Source: InterPro
  • tRNA nucleotidyltransferase activity Source: EcoCyc

GO - Biological processi

Keywordsi

Molecular functionRNA-binding, tRNA-binding
Biological processrRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:EG10863-MONOMER.
MetaCyc:EG10863-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Truncated inactive ribonuclease PH
Short name:
Truncated inactive RNase PH
Alternative name(s):
Inactive RNase PH1 Publication
Truncated RNase PH1 Publication
Gene namesi
Name:rphUniRule annotation
Synonyms:orfE
Ordered Locus Names:b3643, JW3618
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10863. rph.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

Disruption phenotypei

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).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001398891 – 228Truncated inactive ribonuclease PHAdd BLAST228

Proteomic databases

EPDiP0CG19.
PaxDbiP0CG19.

Expressioni

Inductioni

The catalytically inactive protein is present at significantly lower levels than restored wild-type protein (at protein level) (PubMed:28808133).1 Publication

Interactioni

Subunit structurei

Homodimer (By similarity). No interaction between the inactive protein and RppH or RNase P was detected by immunoprecipitation (PubMed:28808133).UniRule annotation1 Publication

Protein-protein interaction databases

DIPiDIP-10738N.
IntActiP0CG19. 9 interactors.
STRINGi511145.b3643.

Structurei

3D structure databases

ProteinModelPortaliP0CG19.
SMRiP0CG19.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni124 – 126Phosphate (substrate) bindingUniRule annotation3

Sequence similaritiesi

Belongs to the RNase PH family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105ED0. Bacteria.
COG0689. LUCA.
InParanoidiP0CG19.

Family and domain databases

CDDicd11362. RNase_PH_bact. 1 hit.
Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00564. RNase_PH. 1 hit.
InterProiView protein in InterPro
IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR036345. ExoRNase_PH_dom2_sf.
IPR027408. PNPase/RNase_PH_dom_sf.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR002381. RNase_PH_bac-type.
IPR018336. RNase_PH_CS.
PfamiView protein in Pfam
PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
TIGRFAMsiTIGR01966. RNasePH. 1 hit.
PROSITEiView protein in PROSITE
PS01277. RIBONUCLEASE_PH. 1 hit.

Sequencei

Sequence statusi: Complete.

P0CG19-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRPAGRSNNQ VRPVTLTRNY TKHAEGSVLV EFGDTKVLCT ASIEEGVPRF
60 70 80 90 100
LKGQGQGWIT AEYGMLPRST HTRNAREAAK GKQGGRTMEI QRLIARALRA
110 120 130 140 150
AVDLKALGEF TITLDCDVLQ ADGGTRTASI TGACVALVDA LQKLVENGKL
160 170 180 190 200
KTNPMKGMVA AVSVGIVNGE AVCDLEYVED SAAETDMNVV MTEDGRIIEV
210 220
QGTAEGEPFT HEELLILLAL ARGESNPL
Length:228
Mass (Da):24,425
Last modified:June 15, 2010 - v1
Checksum:i028BC8F5A6859447
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01578 Genomic DNA. No translation available.
L10328 Genomic DNA. Translation: AAA61996.1.
U00096 Genomic DNA. No translation available.
AP009048 Genomic DNA. No translation available.
X72920 Genomic DNA. No translation available.
PIRiA04470. QQECPE.

Similar proteinsi

Entry informationi

Entry nameiRNPH_ECOLI
AccessioniPrimary (citable) accession number: P0CG19
Secondary accession number(s): A8DYQ0, P03842
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 15, 2010
Last sequence update: June 15, 2010
Last modified: February 28, 2018
This is version 44 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome