ID G4D5W6_9FIRM Unreviewed; 415 AA.
AC G4D5W6;
DT 14-DEC-2011, integrated into UniProtKB/TrEMBL.
DT 14-DEC-2011, sequence version 1.
DT 27-MAR-2024, entry version 67.
DE RecName: Full=Multifunctional fusion protein {ECO:0000256|HAMAP-Rule:MF_00564, ECO:0000256|HAMAP-Rule:MF_01405};
DE Includes:
DE RecName: Full=dITP/XTP pyrophosphatase {ECO:0000256|HAMAP-Rule:MF_01405};
DE EC=3.6.1.66 {ECO:0000256|HAMAP-Rule:MF_01405};
DE AltName: Full=Non-canonical purine NTP pyrophosphatase {ECO:0000256|HAMAP-Rule:MF_01405};
DE AltName: Full=Non-standard purine NTP pyrophosphatase {ECO:0000256|HAMAP-Rule:MF_01405};
DE AltName: Full=Nucleoside-triphosphate diphosphatase {ECO:0000256|HAMAP-Rule:MF_01405};
DE AltName: Full=Nucleoside-triphosphate pyrophosphatase {ECO:0000256|HAMAP-Rule:MF_01405};
DE Short=NTPase {ECO:0000256|HAMAP-Rule:MF_01405};
DE Includes:
DE RecName: Full=Ribonuclease PH {ECO:0000256|HAMAP-Rule:MF_00564};
DE Short=RNase PH {ECO:0000256|HAMAP-Rule:MF_00564};
DE EC=2.7.7.56 {ECO:0000256|HAMAP-Rule:MF_00564};
DE AltName: Full=tRNA nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00564};
GN Name=rnpA2 {ECO:0000313|EMBL:EGY78130.1};
GN Synonyms=rph {ECO:0000256|HAMAP-Rule:MF_00564};
GN ORFNames=HMPREF9129_1796 {ECO:0000313|EMBL:EGY78130.1};
OS Peptoniphilus indolicus ATCC 29427.
OC Bacteria; Bacillota; Tissierellia; Tissierellales; Peptoniphilaceae;
OC Peptoniphilus.
OX NCBI_TaxID=997350 {ECO:0000313|EMBL:EGY78130.1, ECO:0000313|Proteomes:UP000003422};
RN [1] {ECO:0000313|EMBL:EGY78130.1, ECO:0000313|Proteomes:UP000003422}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29427 {ECO:0000313|EMBL:EGY78130.1,
RC ECO:0000313|Proteomes:UP000003422};
RA Muzny D., Qin X., Deng J., Jiang H., Liu Y., Qu J., Song X.-Z., Zhang L.,
RA Thornton R., Coyle M., Francisco L., Jackson L., Javaid M., Korchina V.,
RA Kovar C., Mata R., Mathew T., Ngo R., Nguyen L., Nguyen N., Okwuonu G.,
RA Ongeri F., Pham C., Simmons D., Wilczek-Boney K., Hale W., Jakkamsetti A.,
RA Pham P., Ruth R., San Lucas F., Warren J., Zhang J., Zhao Z., Zhou C.,
RA Zhu D., Lee S., Bess C., Blankenburg K., Forbes L., Fu Q., Gubbala S.,
RA Hirani K., Jayaseelan J.C., Lara F., Munidasa M., Palculict T., Patil S.,
RA Pu L.-L., Saada N., Tang L., Weissenberger G., Zhu Y., Hemphill L.,
RA Shang Y., Youmans B., Ayvaz T., Ross M., Santibanez J., Aqrawi P.,
RA Gross S., Joshi V., Fowler G., Nazareth L., Reid J., Worley K.,
RA Petrosino J., Highlander S., Gibbs R.;
RL Submitted (JUN-2011) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Phosphorolytic 3'-5' exoribonuclease that plays an important
CC role in tRNA 3'-end maturation. Removes nucleotide residues following
CC the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of
CC RNA molecules by using nucleoside diphosphates as substrates, but this
CC may not be physiologically important. Probably plays a role in
CC initiation of 16S rRNA degradation (leading to ribosome degradation)
CC during starvation. {ECO:0000256|HAMAP-Rule:MF_00564}.
CC -!- FUNCTION: Pyrophosphatase that catalyzes the hydrolysis of nucleoside
CC triphosphates to their monophosphate derivatives, with a high
CC preference for the non-canonical purine nucleotides XTP (xanthosine
CC triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to
CC function as a house-cleaning enzyme that removes non-canonical purine
CC nucleotides from the nucleotide pool, thus preventing their
CC incorporation into DNA/RNA and avoiding chromosomal lesions.
CC {ECO:0000256|HAMAP-Rule:MF_01405}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + ITP = diphosphate + H(+) + IMP; Xref=Rhea:RHEA:29399,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58053, ChEBI:CHEBI:61402; EC=3.6.1.66;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + XTP = diphosphate + H(+) + XMP; Xref=Rhea:RHEA:28610,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57464, ChEBI:CHEBI:61314; EC=3.6.1.66;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dITP + H2O = dIMP + diphosphate + H(+); Xref=Rhea:RHEA:28342,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:61194, ChEBI:CHEBI:61382; EC=3.6.1.66;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=phosphate + tRNA(n+1) = a ribonucleoside 5'-diphosphate +
CC tRNA(n); Xref=Rhea:RHEA:10628, Rhea:RHEA-COMP:17343, Rhea:RHEA-
CC COMP:17344, ChEBI:CHEBI:43474, ChEBI:CHEBI:57930, ChEBI:CHEBI:173114;
CC EC=2.7.7.56; Evidence={ECO:0000256|HAMAP-Rule:MF_00564};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01405};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_01405};
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_01405}.
CC -!- SUBUNIT: Homohexameric ring arranged as a trimer of dimers.
CC {ECO:0000256|HAMAP-Rule:MF_00564}.
CC -!- SIMILARITY: Belongs to the HAM1 NTPase family. {ECO:0000256|HAMAP-
CC Rule:MF_01405, ECO:0000256|RuleBase:RU003781}.
CC -!- SIMILARITY: Belongs to the RNase PH family.
CC {ECO:0000256|ARBA:ARBA00006678, ECO:0000256|HAMAP-Rule:MF_00564}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01405}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EGY78130.1}.
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DR EMBL; AGBB01000176; EGY78130.1; -; Genomic_DNA.
DR AlphaFoldDB; G4D5W6; -.
DR STRING; 997350.HMPREF9129_1796; -.
DR PATRIC; fig|997350.3.peg.1722; -.
DR eggNOG; COG0127; Bacteria.
DR eggNOG; COG0689; Bacteria.
DR HOGENOM; CLU_046108_1_1_9; -.
DR OrthoDB; 9807456at2; -.
DR Proteomes; UP000003422; Unassembled WGS sequence.
DR GO; GO:0000175; F:3'-5'-RNA exonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0035870; F:dITP diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0036220; F:ITP diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0017111; F:ribonucleoside triphosphate phosphatase activity; IEA:InterPro.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009022; F:tRNA nucleotidyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0036222; F:XTP diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009146; P:purine nucleoside triphosphate catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016075; P:rRNA catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR CDD; cd00515; HAM1; 1.
DR CDD; cd11362; RNase_PH_bact; 1.
DR Gene3D; 3.90.950.10; -; 1.
DR Gene3D; 3.30.230.70; GHMP Kinase, N-terminal domain; 1.
DR HAMAP; MF_01405; Non_canon_purine_NTPase; 1.
DR HAMAP; MF_00564; RNase_PH; 1.
DR InterPro; IPR020922; dITP/XTP_pyrophosphatase.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR015847; ExoRNase_PH_dom2.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR029001; ITPase-like_fam.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR002637; RdgB/HAM1.
DR InterPro; IPR020568; Ribosomal_Su5_D2-typ_SF.
DR InterPro; IPR002381; RNase_PH_bac-type.
DR NCBIfam; TIGR00042; RdgB/HAM1 family non-canonical purine NTP pyrophosphatase; 1.
DR NCBIfam; TIGR01966; RNasePH; 1.
DR PANTHER; PTHR11953; EXOSOME COMPLEX COMPONENT; 1.
DR PANTHER; PTHR11953:SF2; EXOSOME COMPLEX COMPONENT MTR3; 1.
DR Pfam; PF01725; Ham1p_like; 1.
DR Pfam; PF01138; RNase_PH; 1.
DR Pfam; PF03725; RNase_PH_C; 1.
DR SUPFAM; SSF52972; ITPase-like; 1.
DR SUPFAM; SSF55666; Ribonuclease PH domain 2-like; 1.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
PE 3: Inferred from homology;
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_01405};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01405};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01405}; Nucleotide metabolism {ECO:0000256|HAMAP-Rule:MF_01405};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01405}; Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_00564};
KW Reference proteome {ECO:0000313|Proteomes:UP000003422};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW Rule:MF_00564};
KW rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW Rule:MF_00564}; Transferase {ECO:0000256|HAMAP-Rule:MF_00564};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_00564};
KW tRNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW Rule:MF_00564}.
FT DOMAIN 9..139
FT /note="Exoribonuclease phosphorolytic"
FT /evidence="ECO:0000259|Pfam:PF01138"
FT DOMAIN 158..222
FT /note="Exoribonuclease phosphorolytic"
FT /evidence="ECO:0000259|Pfam:PF03725"
FT ACT_SITE 308
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 85
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
FT BINDING 123..125
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /ligand_note="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00564"
FT BINDING 245..250
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 279
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 308
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 309
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 390..393
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
FT BINDING 413
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01405"
SQ SEQUENCE 415 AA; 46601 MW; E0FCB16791C27BB4 CRC64;
MRKDRNNNEM RNIKIQNNYL NHPDGSVLIE CGNTKIICTA MIEDKVPFFL KGKNTGWLSS
EYSMLPGSTD TRKVRDSSRG KIDGRSQEIQ RLIGRSLRQA IDLSKIGERT IWIDCDVISA
DGGTRTTSIN GAYVALKLAV DKYIEKGIFN EDPIISKIAA LSVGVVNGEN LVDLCYKEDS
KADVDLNLVI NDKFEFIEIQ GTAEGRPFSL DRLNQLLDLS KESFNKIFEI QEKATKKAKK
IVLSTDNAHK VEEINKILEG LDVQILTKSE ILKSNLEVEE NSDTLQGNAH LKAVEMKKYT
NYAVIADDTG LFVDELNGEP GVKSARYNEK FDHNDTENRK LLLKNLEKSS NRKAKFKTVI
AYIGENNEEI FFEGVCKGDI IKSEKGDAGF GYDSIFVPKG YDKTFAELGN EEKIK
//
