NTPPA_ECOLI
ID NTPPA_ECOLI Reviewed; 197 AA.
AC P25536; Q2M8W6;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=dTTP/UTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000305};
DE Short=dTTPase/UTPase {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000303|PubMed:26252214};
DE EC=3.6.1.9 {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000269|PubMed:24210219, ECO:0000269|PubMed:25658941, ECO:0000269|PubMed:28811554};
DE AltName: Full=Nucleoside triphosphate pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000303|PubMed:24210219};
DE AltName: Full=Nucleotide pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000303|PubMed:24210219};
DE Short=Nucleotide PPase {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000303|PubMed:25658941};
GN Name=yhdE; OrderedLocusNames=b3248, JW3217;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1937035; DOI=10.1016/0378-1119(91)90578-y;
RA Wachi M., Doi M., Ueda T., Ueki M., Tsuritani K., Nagai K., Matsuhashi M.;
RT "Sequence of the downstream flanking region of the shape-determining genes
RT mreBCD of Escherichia coli.";
RL Gene 106:135-136(1991).
RN [2]
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 [3]
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 [4]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF SER-8; SER-10; ARG-12; ARG-13;
RP GLU-32; GLU-33; LYS-52; ASP-70; GLU-81; LYS-82; TYR-150 AND GLN-153.
RX PubMed=24210219; DOI=10.1016/j.chembiol.2013.09.011;
RA Tchigvintsev A., Tchigvintsev D., Flick R., Popovic A., Dong A., Xu X.,
RA Brown G., Lu W., Wu H., Cui H., Dombrowski L., Joo J.C., Beloglazova N.,
RA Min J., Savchenko A., Caudy A.A., Rabinowitz J.D., Murzin A.G.,
RA Yakunin A.F.;
RT "Biochemical and structural studies of conserved Maf proteins revealed
RT nucleotide pyrophosphatases with a preference for modified nucleotides.";
RL Chem. Biol. 20:1386-1398(2013).
RN [6]
RP SUBUNIT, AND MOLECULAR DYNAMICS SIMULATION.
RX PubMed=26252214; DOI=10.1371/journal.pone.0134879;
RA Wang N., Jiang J., Li X., Tan H., Zheng J., Chen G., Jia Z.;
RT "Molecular dynamics simulation studies of dTTP binding and catalysis
RT mediated by YhdE dimerization.";
RL PLoS ONE 10:E0134879-E0134879(2015).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF GLU-33.
RX PubMed=28811554; DOI=10.1038/s41598-017-08368-1;
RA Shen Q., Tan H., Xing G.W., Zheng J., Jia Z.;
RT "A new method to investigate the catalytic mechanism of YhdE
RT pyrophosphatase by using a pyrophosphate fluorescence probe.";
RL Sci. Rep. 7:8169-8169(2017).
RN [8] {ECO:0007744|PDB:4P0E}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-190 OF MUTANT ALA-33, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=25658941; DOI=10.1371/journal.pone.0117823;
RA Jin J., Wu R., Zhu J., Yang S., Lei Z., Wang N., Singh V.K., Zheng J.,
RA Jia Z.;
RT "Insights into the cellular function of YhdE, a nucleotide pyrophosphatase
RT from Escherichia coli.";
RL PLoS ONE 10:E0117823-E0117823(2015).
CC -!- FUNCTION: Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP
CC and UTP (PubMed:24210219, PubMed:25658941, PubMed:28811554). Can also
CC hydrolyze TTP and the modified nucleotides 5-methyl-UTP (m(5)UTP),
CC pseudo-UTP and 5-methyl-CTP (m(5)CTP). Has weak activity with CTP
CC (PubMed:24210219, PubMed:25658941). May have a dual role in cell
CC division arrest and in preventing the incorporation of modified
CC nucleotides into cellular nucleic acids (PubMed:24210219,
CC PubMed:25658941). Important in maintenance of cell shape
CC (PubMed:25658941). {ECO:0000269|PubMed:24210219,
CC ECO:0000269|PubMed:25658941, ECO:0000269|PubMed:28811554}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTTP + H2O = diphosphate + dTMP + H(+); Xref=Rhea:RHEA:28534,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37568, ChEBI:CHEBI:63528; EC=3.6.1.9;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00528,
CC ECO:0000269|PubMed:24210219, ECO:0000269|PubMed:25658941,
CC ECO:0000269|PubMed:28811554};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + UTP = diphosphate + H(+) + UMP; Xref=Rhea:RHEA:29395,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:46398, ChEBI:CHEBI:57865; EC=3.6.1.9;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00528,
CC ECO:0000269|PubMed:24210219, ECO:0000269|PubMed:25658941,
CC ECO:0000269|PubMed:28811554};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + TTP = 5-methyl-UMP + diphosphate + H(+);
CC Xref=Rhea:RHEA:58736, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:63527, ChEBI:CHEBI:142797;
CC Evidence={ECO:0000269|PubMed:24210219};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + psi-UTP = diphosphate + H(+) + psi-UMP;
CC Xref=Rhea:RHEA:58740, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58380, ChEBI:CHEBI:142798;
CC Evidence={ECO:0000269|PubMed:24210219};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methyl-CTP + H2O = 5-methyl-CMP + diphosphate + H(+);
CC Xref=Rhea:RHEA:58732, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:142795, ChEBI:CHEBI:142796;
CC Evidence={ECO:0000269|PubMed:24210219};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00528,
CC ECO:0000269|PubMed:24210219};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=53.0 uM for dTTP {ECO:0000269|PubMed:24210219};
CC KM=0.09 mM for dTTP {ECO:0000269|PubMed:25658941};
CC KM=69.1 uM for UTP {ECO:0000269|PubMed:24210219};
CC KM=0.5 mM for UTP {ECO:0000269|PubMed:25658941};
CC KM=105.9 uM for CTP {ECO:0000269|PubMed:24210219};
CC KM=32.0 uM for m(5)UTP {ECO:0000269|PubMed:24210219};
CC KM=44.8 uM for m(5)CTP {ECO:0000269|PubMed:24210219};
CC KM=47.2 uM for pseudo-UTP {ECO:0000269|PubMed:24210219};
CC Note=kcat is 15.4 sec(-1) with dTTP as substrate. kcat is 15.2 sec(-
CC 1) with UTP as substrate. kcat is 4.9 sec(-1) with CTP as substrate.
CC kcat is 18.2 sec(-1) with m(5)UTP as substrate. kcat is 9.2 sec(-1)
CC with m(5)CTP as substrate. kcat is 10.5 sec(-1) with pseudo-UTP as
CC substrate (PubMed:24210219). kcat is 43 sec(-1) with dTTP as
CC substrate. kcat is 95 sec(-1) with UTP as substrate
CC (PubMed:25658941). {ECO:0000269|PubMed:24210219,
CC ECO:0000269|PubMed:25658941};
CC -!- SUBUNIT: Homodimer (PubMed:24210219, PubMed:25658941, PubMed:26252214).
CC Can also form homotetramers (PubMed:24210219).
CC {ECO:0000269|PubMed:24210219, ECO:0000269|PubMed:25658941,
CC ECO:0000269|PubMed:26252214}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00528,
CC ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Knockout mutant grows faster than the wild-type
CC and exhibits a more spherical shape. {ECO:0000269|PubMed:25658941}.
CC -!- SIMILARITY: Belongs to the Maf family. YhdE subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00528, ECO:0000305|PubMed:24210219}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA58051.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X57166; CAA40456.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58051.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76280.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77290.1; -; Genomic_DNA.
DR PIR; JQ1271; JQ1271.
DR RefSeq; NP_417714.1; NC_000913.3.
DR RefSeq; WP_000203105.1; NZ_SSZK01000034.1.
DR PDB; 4P0E; X-ray; 2.30 A; A/B=2-190.
DR PDBsum; 4P0E; -.
DR AlphaFoldDB; P25536; -.
DR SMR; P25536; -.
DR BioGRID; 4262448; 147.
DR BioGRID; 852065; 1.
DR IntAct; P25536; 4.
DR STRING; 511145.b3248; -.
DR jPOST; P25536; -.
DR PaxDb; P25536; -.
DR PRIDE; P25536; -.
DR EnsemblBacteria; AAC76280; AAC76280; b3248.
DR EnsemblBacteria; BAE77290; BAE77290; BAE77290.
DR GeneID; 947753; -.
DR KEGG; ecj:JW3217; -.
DR KEGG; eco:b3248; -.
DR PATRIC; fig|1411691.4.peg.3481; -.
DR EchoBASE; EB1275; -.
DR eggNOG; COG0424; Bacteria.
DR HOGENOM; CLU_040416_2_1_6; -.
DR InParanoid; P25536; -.
DR OMA; RIDGDFY; -.
DR PhylomeDB; P25536; -.
DR BioCyc; EcoCyc:EG11298-MON; -.
DR BioCyc; MetaCyc:EG11298-MON; -.
DR BRENDA; 3.6.1.9; 2026.
DR PRO; PR:P25536; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0036218; F:dTTP diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0030145; F:manganese ion binding; IDA:EcoCyc.
DR GO; GO:0035529; F:NADH pyrophosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0047429; F:nucleoside-triphosphate diphosphatase activity; IDA:EcoliWiki.
DR GO; GO:0036221; F:UTP diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
DR CDD; cd00555; Maf; 1.
DR Gene3D; 3.90.950.10; -; 1.
DR HAMAP; MF_00528; Maf; 1.
DR InterPro; IPR029001; ITPase-like_fam.
DR InterPro; IPR003697; Maf-like.
DR PANTHER; PTHR43213; PTHR43213; 1.
DR Pfam; PF02545; Maf; 1.
DR PIRSF; PIRSF006305; Maf; 1.
DR SUPFAM; SSF52972; SSF52972; 1.
DR TIGRFAMs; TIGR00172; maf; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Nucleotide metabolism;
KW Reference proteome.
FT CHAIN 1..197
FT /note="dTTP/UTP pyrophosphatase"
FT /id="PRO_0000122981"
FT ACT_SITE 70
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00528,
FT ECO:0000305|PubMed:24210219"
FT SITE 12
FT /note="Important for substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00528,
FT ECO:0000305|PubMed:24210219"
FT SITE 71
FT /note="Important for substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00528,
FT ECO:0000305|PubMed:24210219"
FT SITE 153
FT /note="Important for substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00528,
FT ECO:0000305|PubMed:24210219"
FT MUTAGEN 8
FT /note="S->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 10
FT /note="S->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 12
FT /note="R->A: Slight decrease in activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 13
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 32
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 33
FT /note="E->A: Loss of activity. Has weak pyrophosphatase
FT activity when assayed using PPi fluorescence sensor."
FT /evidence="ECO:0000269|PubMed:24210219,
FT ECO:0000269|PubMed:28811554"
FT MUTAGEN 52
FT /note="K->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 70
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 81
FT /note="E->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 82
FT /note="K->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 150
FT /note="Y->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 153
FT /note="Q->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT MUTAGEN 153
FT /note="Q->E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24210219"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 11..19
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 41..58
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 66..75
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 86..96
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 100..110
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 115..126
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 131..138
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 155..159
FT /evidence="ECO:0007829|PDB:4P0E"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 167..171
FT /evidence="ECO:0007829|PDB:4P0E"
FT HELIX 175..188
FT /evidence="ECO:0007829|PDB:4P0E"
SQ SEQUENCE 197 AA; 21515 MW; D023A366FB71DA87 CRC64;
MTSLYLASGS PRRQELLAQL GVTFERIVTG IEEQRQPQES AQQYVVRLAR EKARAGVAQT
AKDLPVLGAD TIVILNGEVL EKPRDAEHAA QMLRKLSGQT HQVMTAVALA DSQHILDCLV
VTDVTFRTLT DEDIAGYVAS DEPLDKAGAY GIQGLGGCFV RKINGSYHAV VGLPLVETYE
LLSNFNALRE KRDKHDG
