RPPH_ECOLI
ID RPPH_ECOLI Reviewed; 176 AA.
AC P0A776; Q2MA07; Q46930;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=RNA pyrophosphohydrolase;
DE EC=3.6.1.- {ECO:0000269|PubMed:11479323};
DE AltName: Full=(Di)nucleoside polyphosphate hydrolase;
DE AltName: Full=Ap5A pyrophosphatase;
GN Name=rppH {ECO:0000303|PubMed:18202662}; Synonyms=nudH, ygdP;
GN OrderedLocusNames=b2830, JW2798;
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=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 [2]
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 [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RC STRAIN=K12;
RX PubMed=11479323; DOI=10.1074/jbc.m107032200;
RA Bessman M.J., Walsh J.D., Dunn C.A., Swaminathan J., Weldon J.E., Shen J.;
RT "The gene ygdP, associated with the invasiveness of Escherichia coli K1,
RT designates a Nudix hydrolase, Orf176, active on adenosine (5')-
RT pentaphospho-(5')-adenosine (Ap5A).";
RL J. Biol. Chem. 276:37834-37838(2001).
RN [4]
RP FUNCTION IN PATHOGENIC STRAIN K1.
RX PubMed=10760174; DOI=10.1046/j.1365-2958.2000.01840.x;
RA Badger J.L., Wass C.A., Kim K.S.;
RT "Identification of Escherichia coli K1 genes contributing to human brain
RT microvascular endothelial cell invasion by differential fluorescence
RT induction.";
RL Mol. Microbiol. 36:174-182(2000).
RN [5]
RP FUNCTION AS A RNA PYROPHOSPHOHYDROLASE, AND MUTAGENESIS OF GLU-53.
RX PubMed=18202662; DOI=10.1038/nature06475;
RA Deana A., Celesnik H., Belasco J.G.;
RT "The bacterial enzyme RppH triggers messenger RNA degradation by 5'
RT pyrophosphate removal.";
RL Nature 451:355-358(2008).
RN [6]
RP FUNCTION IN TRNA PROCESSING, SUBUNIT, 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: Master regulator of 5'-end-dependent mRNA decay
CC (PubMed:18202662). Accelerates the degradation of transcripts by
CC removing pyrophosphate from the 5'-end of triphosphorylated RNA,
CC leading to a more labile monophosphorylated state that can stimulate
CC subsequent ribonuclease cleavage (PubMed:18202662). Preferentially
CC hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction
CC products (PubMed:11479323). Also able to hydrolyze diadenosine
CC hexa- and tetra-phosphate (PubMed:11479323). Has no activity on
CC diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose
CC (PubMed:11479323). In an RNase PH (rph) wild-type strain background,
CC RppH is not required for maturation of tRNAs; however, strains with the
CC truncated rph allele (for example K12 W1485 and its derivatives MG1655
CC and W3110) require RppH for maturation of certain monocistronic tRNAs
CC with short (<5 nucleotides) leader sequences (PubMed:28808133). In the
CC meningitis causing strain E.coli K1, has been shown to play a role in
CC HBMEC (human brain microvascular endothelial cells) invasion in vitro
CC (PubMed:10760174). {ECO:0000269|PubMed:10760174,
CC ECO:0000269|PubMed:11479323, ECO:0000269|PubMed:18202662,
CC ECO:0000269|PubMed:28808133}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11479323};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11479323};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11479323};
CC Note=Magnesium or zinc. Manganese can be used to a lesser extent.
CC {ECO:0000269|PubMed:11479323};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.5-9.0. {ECO:0000269|PubMed:11479323};
CC -!- SUBUNIT: Monomer (PubMed:11479323). No interaction between this protein
CC and catalytically inactive RNase PH was detected by immunoprecipitation
CC (PubMed:28808133). {ECO:0000269|PubMed:11479323,
CC ECO:0000269|PubMed:28808133}.
CC -!- DISRUPTION PHENOTYPE: Altered 5'-processing of primary pre-tRNA
CC transcripts with short (<5 nucleotides) leaders; in the presence of the
CC truncated inactive allele encoded by rph in strains derived from K12
CC W1485, including strains MG1655 and W3110 (PubMed:28808133). In the
CC presence of wild-type (catalytically active) RNase PH no effect on
CC processing (PubMed:28808133). No effect on growth rate, a slightly
CC stronger effect is seen when combined with the inactive rph allele
CC (PubMed:28808133). {ECO:0000269|PubMed:28808133}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. RppH subfamily.
CC {ECO:0000305}.
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DR EMBL; U29581; AAB40477.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75869.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76899.1; -; Genomic_DNA.
DR PIR; G65065; G65065.
DR RefSeq; NP_417307.1; NC_000913.3.
DR RefSeq; WP_000564489.1; NZ_STEB01000034.1.
DR PDB; 2KDV; NMR; -; A=1-164.
DR PDB; 2KDW; NMR; -; A=1-164.
DR PDB; 4S2V; X-ray; 1.70 A; A=1-156.
DR PDB; 4S2W; X-ray; 1.99 A; A=1-158.
DR PDB; 4S2X; X-ray; 1.50 A; A=1-158.
DR PDB; 4S2Y; X-ray; 1.60 A; A=1-158.
DR PDB; 5YGU; X-ray; 2.30 A; B=1-158.
DR PDB; 6VCK; X-ray; 2.69 A; B=1-160.
DR PDB; 6VCL; X-ray; 2.06 A; B=1-160.
DR PDB; 6VCM; X-ray; 2.35 A; B=1-160.
DR PDB; 6VCN; X-ray; 1.90 A; A=1-160.
DR PDB; 6VCO; X-ray; 1.70 A; A=1-160.
DR PDB; 6VCP; X-ray; 1.70 A; A=1-160.
DR PDB; 6VCQ; X-ray; 1.60 A; A=1-160.
DR PDB; 6VCR; X-ray; 1.60 A; A=1-160.
DR PDBsum; 2KDV; -.
DR PDBsum; 2KDW; -.
DR PDBsum; 4S2V; -.
DR PDBsum; 4S2W; -.
DR PDBsum; 4S2X; -.
DR PDBsum; 4S2Y; -.
DR PDBsum; 5YGU; -.
DR PDBsum; 6VCK; -.
DR PDBsum; 6VCL; -.
DR PDBsum; 6VCM; -.
DR PDBsum; 6VCN; -.
DR PDBsum; 6VCO; -.
DR PDBsum; 6VCP; -.
DR PDBsum; 6VCQ; -.
DR PDBsum; 6VCR; -.
DR AlphaFoldDB; P0A776; -.
DR SMR; P0A776; -.
DR BioGRID; 4263204; 49.
DR BioGRID; 851628; 2.
DR DIP; DIP-47855N; -.
DR IntAct; P0A776; 55.
DR STRING; 511145.b2830; -.
DR jPOST; P0A776; -.
DR PaxDb; P0A776; -.
DR PRIDE; P0A776; -.
DR EnsemblBacteria; AAC75869; AAC75869; b2830.
DR EnsemblBacteria; BAE76899; BAE76899; BAE76899.
DR GeneID; 66673303; -.
DR GeneID; 947300; -.
DR KEGG; ecj:JW2798; -.
DR KEGG; eco:b2830; -.
DR PATRIC; fig|1411691.4.peg.3905; -.
DR EchoBASE; EB2896; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_087195_3_2_6; -.
DR InParanoid; P0A776; -.
DR OMA; PCVGIML; -.
DR PhylomeDB; P0A776; -.
DR BioCyc; EcoCyc:G7459-MON; -.
DR BioCyc; MetaCyc:G7459-MON; -.
DR BRENDA; 3.6.1.61; 2026.
DR EvolutionaryTrace; P0A776; -.
DR PRO; PR:P0A776; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016818; F:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; IDA:EcoliWiki.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0110153; F:RNA NAD-cap (NMN-forming) hydrolase activity; IDA:UniProtKB.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IDA:EcoCyc.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
DR GO; GO:0110155; P:NAD-cap decapping; IDA:UniProtKB.
DR GO; GO:0110154; P:RNA decapping; IDA:EcoCyc.
DR GO; GO:0050779; P:RNA destabilization; IMP:EcoliWiki.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR CDD; cd03671; Ap4A_hydrolase_plant_like; 1.
DR HAMAP; MF_00298; Nudix_RppH; 1.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR022927; RppH.
DR Pfam; PF00293; NUDIX; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Manganese; Reference proteome;
KW tRNA processing; Zinc.
FT CHAIN 1..176
FT /note="RNA pyrophosphohydrolase"
FT /id="PRO_0000057005"
FT DOMAIN 6..149
FT /note="Nudix hydrolase"
FT MOTIF 38..59
FT /note="Nudix box"
FT MUTAGEN 53
FT /note="E->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:18202662"
FT STRAND 6..16
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 18..27
FT /evidence="ECO:0007829|PDB:4S2X"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:2KDW"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:2KDW"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 46..58
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:6VCQ"
FT STRAND 94..104
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:4S2X"
FT STRAND 120..128
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:4S2X"
FT HELIX 141..159
FT /evidence="ECO:0007829|PDB:4S2X"
SQ SEQUENCE 176 AA; 20795 MW; AF701FE93450C6D4 CRC64;
MIDDDGYRPN VGIVICNRQG QVMWARRFGQ HSWQFPQGGI NPGESAEQAM YRELFEEVGL
SRKDVRILAS TRNWLRYKLP KRLVRWDTKP VCIGQKQKWF LLQLVSGDAE INMQTSSTPE
FDGWRWVSYW YPVRQVVSFK RDVYRRVMKE FASVVMSLQE NTPKPQNASA YRRKRG
