Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNA pyrophosphohydrolase

Gene

rppH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.2 Publications

Cofactori

Mg2+1 Publication, Zn2+1 Publication, Mn2+1 PublicationNote: Magnesium or zinc. Manganese can be used to a lesser extent.1 Publication

pH dependencei

Optimum pH is 8.5-9.0.

GO - Molecular functioni

  • hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides Source: EcoliWiki
  • metal ion binding Source: UniProtKB-HAMAP
  • RNA pyrophosphohydrolase activity Source: EcoCyc

GO - Biological processi

  • mRNA catabolic process Source: EcoCyc
  • RNA destabilization Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Manganese, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G7459-MONOMER.
ECOL316407:JW2798-MONOMER.
MetaCyc:G7459-MONOMER.
BRENDAi3.6.1.61. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA pyrophosphohydrolase (EC:3.6.1.-)
Alternative name(s):
(Di)nucleoside polyphosphate hydrolase
Ap5A pyrophosphatase
Gene namesi
Name:rppH
Synonyms:nudH, ygdP
Ordered Locus Names:b2830, JW2798
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13091. nudH.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi53 – 531E → A: Loss of function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 176176RNA pyrophosphohydrolasePRO_0000057005Add
BLAST

Proteomic databases

PaxDbiP0A776.
PRIDEiP0A776.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4263204. 41 interactions.
DIPiDIP-47855N.
IntActiP0A776. 55 interactions.
STRINGi511145.b2830.

Structurei

Secondary structure

1
176
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 1611Combined sources
Beta strandi18 – 2710Combined sources
Turni28 – 303Combined sources
Beta strandi32 – 343Combined sources
Beta strandi37 – 393Combined sources
Helixi46 – 5813Combined sources
Helixi62 – 643Combined sources
Beta strandi65 – 706Combined sources
Beta strandi75 – 784Combined sources
Helixi81 – 833Combined sources
Beta strandi88 – 903Combined sources
Beta strandi94 – 10411Combined sources
Helixi108 – 1103Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi120 – 1289Combined sources
Helixi131 – 1355Combined sources
Helixi138 – 1403Combined sources
Helixi141 – 15818Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2KDVNMR-A1-164[»]
2KDWNMR-A1-164[»]
4S2VX-ray1.70A1-156[»]
4S2WX-ray1.99A1-158[»]
4S2XX-ray1.50A1-158[»]
4S2YX-ray1.60A1-158[»]
ProteinModelPortaliP0A776.
SMRiP0A776. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A776.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 149144Nudix hydrolaseAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi38 – 5922Nudix boxAdd
BLAST

Sequence similaritiesi

Belongs to the Nudix hydrolase family. RppH subfamily.Curated
Contains 1 nudix hydrolase domain.Curated

Phylogenomic databases

eggNOGiENOG4105EJF. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000066723.
InParanoidiP0A776.
KOiK08311.
OMAiERNEVFW.
OrthoDBiEOG6Q2SKR.
PhylomeDBiP0A776.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00298. Nudix_RppH.
InterProiIPR020476. Nudix_hydrolase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR022927. RppH.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR00502. NUDIXFAMILY.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A776-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDDDGYRPN VGIVICNRQG QVMWARRFGQ HSWQFPQGGI NPGESAEQAM
60 70 80 90 100
YRELFEEVGL SRKDVRILAS TRNWLRYKLP KRLVRWDTKP VCIGQKQKWF
110 120 130 140 150
LLQLVSGDAE INMQTSSTPE FDGWRWVSYW YPVRQVVSFK RDVYRRVMKE
160 170
FASVVMSLQE NTPKPQNASA YRRKRG
Length:176
Mass (Da):20,795
Last modified:June 7, 2005 - v1
Checksum:iAF701FE93450C6D4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40477.1.
U00096 Genomic DNA. Translation: AAC75869.1.
AP009048 Genomic DNA. Translation: BAE76899.1.
PIRiG65065.
RefSeqiNP_417307.1. NC_000913.3.
WP_000564489.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75869; AAC75869; b2830.
BAE76899; BAE76899; BAE76899.
GeneIDi947300.
KEGGiecj:JW2798.
eco:b2830.
PATRICi32121078. VBIEscCol129921_2928.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40477.1.
U00096 Genomic DNA. Translation: AAC75869.1.
AP009048 Genomic DNA. Translation: BAE76899.1.
PIRiG65065.
RefSeqiNP_417307.1. NC_000913.3.
WP_000564489.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2KDVNMR-A1-164[»]
2KDWNMR-A1-164[»]
4S2VX-ray1.70A1-156[»]
4S2WX-ray1.99A1-158[»]
4S2XX-ray1.50A1-158[»]
4S2YX-ray1.60A1-158[»]
ProteinModelPortaliP0A776.
SMRiP0A776. Positions 1-164.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263204. 41 interactions.
DIPiDIP-47855N.
IntActiP0A776. 55 interactions.
STRINGi511145.b2830.

Proteomic databases

PaxDbiP0A776.
PRIDEiP0A776.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75869; AAC75869; b2830.
BAE76899; BAE76899; BAE76899.
GeneIDi947300.
KEGGiecj:JW2798.
eco:b2830.
PATRICi32121078. VBIEscCol129921_2928.

Organism-specific databases

EchoBASEiEB2896.
EcoGeneiEG13091. nudH.

Phylogenomic databases

eggNOGiENOG4105EJF. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000066723.
InParanoidiP0A776.
KOiK08311.
OMAiERNEVFW.
OrthoDBiEOG6Q2SKR.
PhylomeDBiP0A776.

Enzyme and pathway databases

BioCyciEcoCyc:G7459-MONOMER.
ECOL316407:JW2798-MONOMER.
MetaCyc:G7459-MONOMER.
BRENDAi3.6.1.61. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A776.
PROiP0A776.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00298. Nudix_RppH.
InterProiIPR020476. Nudix_hydrolase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR022927. RppH.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR00502. NUDIXFAMILY.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5')-pentaphospho-(5')-adenosine (Ap5A)."
    Bessman M.J., Walsh J.D., Dunn C.A., Swaminathan J., Weldon J.E., Shen J.
    J. Biol. Chem. 276:37834-37838(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, COFACTOR, SUBUNIT.
    Strain: K12.
  4. "Identification of Escherichia coli K1 genes contributing to human brain microvascular endothelial cell invasion by differential fluorescence induction."
    Badger J.L., Wass C.A., Kim K.S.
    Mol. Microbiol. 36:174-182(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PATHOGENIC STRAIN K1.
  5. "The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal."
    Deana A., Celesnik H., Belasco J.G.
    Nature 451:355-358(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A RNA PYROPHOSPHOHYDROLASE, MUTAGENESIS OF GLU-53.

Entry informationi

Entry nameiRPPH_ECOLI
AccessioniPrimary (citable) accession number: P0A776
Secondary accession number(s): Q2MA07, Q46930
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: April 13, 2016
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.