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Protein

Ribonuclease PH

Gene

rph

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation.UniRule annotation

Catalytic activityi

tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei87Phosphate (substrate) bindingUniRule annotation1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionNucleotidyltransferase, RNA-binding, Transferase, tRNA-binding
Biological processrRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciPAER208964:G1FZ6-5456-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease PHUniRule annotation (EC:2.7.7.56UniRule annotation)
Short name:
RNase PHUniRule annotation
Alternative name(s):
tRNA nucleotidyltransferaseUniRule annotation
Gene namesi
Name:rphUniRule annotation
Ordered Locus Names:PA5334
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA5334

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi69 – 77RSTGERNQR → SSTGERNQS: No longer forms hexamers, no exonuclease activity, does not bind pre-tRNA. 1 Publication9
Mutagenesisi69R → S: Still forms hexamers, wild-type exonuclease activity at 30 degrees Celsius, nearly wild-type at 50 degrees Celsius, decreased binding of pre-tRNA. 1 Publication1
Mutagenesisi74 – 77RNQR → SNQS: No longer forms hexamers, no exonuclease activity, does not bind pre-tRNA. 1 Publication4
Mutagenesisi74R → S: No longer forms hexamers, no exonuclease activity, does not bind pre-tRNA. 1 Publication1
Mutagenesisi77R → S: Still forms hexamers, no exonuclease activity, does not bind pre-tRNA. 1 Publication1
Mutagenesisi127R → A: Still forms hexamers, wild-type exonuclease activity at 30 degrees Celsius, significantly reduced activity at 50 degrees Celsius, binds pre-tRNA. 1 Publication1

Chemistry databases

DrugBankiDB03309 N-Cyclohexyltaurine

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399241 – 239Ribonuclease PHAdd BLAST239

Proteomic databases

PaxDbiP50597
PRIDEiP50597

Interactioni

Subunit structurei

Homohexameric ring arranged as a trimer of dimers; dimeric protein does not seem to be catalytically active (PubMed:14573594).UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi208964.PA5334

Structurei

Secondary structure

1239
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 20Combined sources6
Beta strandi22 – 33Combined sources12
Beta strandi36 – 47Combined sources12
Beta strandi59 – 66Combined sources8
Beta strandi70 – 73Combined sources4
Helixi78 – 81Combined sources4
Helixi86 – 101Combined sources16
Helixi105 – 107Combined sources3
Beta strandi110 – 121Combined sources12
Helixi126 – 147Combined sources22
Beta strandi160 – 168Combined sources9
Beta strandi171 – 175Combined sources5
Helixi178 – 183Combined sources6
Beta strandi185 – 193Combined sources9
Beta strandi198 – 208Combined sources11
Helixi212 – 237Combined sources26

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1R6LX-ray1.90A1-239[»]
1R6MX-ray2.00A1-239[»]
ProteinModelPortaliP50597
SMRiP50597
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50597

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni125 – 127Phosphate (substrate) bindingUniRule annotation1 Publication3

Sequence similaritiesi

Belongs to the RNase PH family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105ED0 Bacteria
COG0689 LUCA
HOGENOMiHOG000229516
InParanoidiP50597
KOiK00989
OMAiKGKGQGW
PhylomeDBiP50597

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.

P50597-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNRPSGRAAD QLRPIRITRH YTKHAEGSVL VEFGDTKVIC TVSAESGVPR
60 70 80 90 100
FLKGQGQGWL TAEYGMLPRS TGERNQREAS RGKQGGRTLE IQRLIGRSLR
110 120 130 140 150
AALDLSKLGE NTLYIDCDVI QADGGTRTAS ITGATVALID ALAVLKKRGA
160 170 180 190 200
LKGNPLKQMV AAVSVGIYQG VPVLDLDYLE DSAAETDLNV VMTDAGGFIE
210 220 230
VQGTAEGAPF RPAELNAMLE LAQQGMQELF ELQRAALAE
Length:239
Mass (Da):25,654
Last modified:December 8, 2000 - v2
Checksum:i76F4717C31261EF7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti68P → R in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti96G → D in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti122A → T in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti137A → S in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti149G → V in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti159M → I in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti186T → S in AAC44429 (PubMed:8824606).Curated1
Sequence conflicti195 – 197AGG → CRR in AAC44429 (PubMed:8824606).Curated3
Sequence conflicti230 – 232FEL → VRT in AAC44429 (PubMed:8824606).Curated3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38241 Genomic DNA Translation: AAC44429.1
AE004091 Genomic DNA Translation: AAG08719.1
PIRiD82978
RefSeqiNP_254021.1, NC_002516.2
WP_003096595.1, NC_002516.2

Genome annotation databases

EnsemblBacteriaiAAG08719; AAG08719; PA5334
GeneIDi878218
KEGGipae:PA5334
PATRICifig|208964.12.peg.5589

Similar proteinsi

Entry informationi

Entry nameiRNPH_PSEAE
AccessioniPrimary (citable) accession number: P50597
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: December 8, 2000
Last modified: April 25, 2018
This is version 110 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health