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dITP/XTP pyrophosphatase (EC 3.6.1.66) (Hypoxanthine/xanthine dNTP pyrophosphatase) (Non-canonical purine NTP pyrophosphatase) (Non-standard purine NTP pyrophosphatase) (Nucleoside-triphosphate diphosphatase) (Nucleoside-triphosphate pyrophosphatase) (NTPase) (Nucleotide triphosphatase)

 IXTPA_METJA             Reviewed;         185 AA.
Q57679;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
28-JUN-2011, sequence version 2.
28-MAR-2018, entry version 122.
RecName: Full=dITP/XTP pyrophosphatase {ECO:0000305|PubMed:11452035};
EC=3.6.1.66 {ECO:0000269|PubMed:11452035};
AltName: Full=Hypoxanthine/xanthine dNTP pyrophosphatase {ECO:0000303|PubMed:11452035};
AltName: Full=Non-canonical purine NTP pyrophosphatase {ECO:0000305|PubMed:11452035};
AltName: Full=Non-standard purine NTP pyrophosphatase {ECO:0000305|PubMed:11452035};
AltName: Full=Nucleoside-triphosphate diphosphatase {ECO:0000305|PubMed:10404228};
AltName: Full=Nucleoside-triphosphate pyrophosphatase {ECO:0000303|PubMed:10404228};
Short=NTPase {ECO:0000303|PubMed:10404228};
AltName: Full=Nucleotide triphosphatase {ECO:0000303|PubMed:10404228};
OrderedLocusNames=MJ0226;
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 /
JCM 10045 / NBRC 100440) (Methanococcus jannaschii).
Archaea; Euryarchaeota; Methanococci; Methanococcales;
Methanocaldococcaceae; Methanocaldococcus.
NCBI_TaxID=243232;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
PubMed=8688087; DOI=10.1126/science.273.5278.1058;
Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D.,
Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D.,
Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I.,
Overbeek R., Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A.,
Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D.,
Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C.,
Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M.,
Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
"Complete genome sequence of the methanogenic archaeon, Methanococcus
jannaschii.";
Science 273:1058-1073(1996).
[2]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY,
BIOPHYSICOCHEMICAL PROPERTIES, AND COFACTOR.
PubMed=11452035; DOI=10.1093/nar/29.14.3099;
Chung J.H., Back J.H., Park Y.I., Han Y.S.;
"Biochemical characterization of a novel hypoxanthine/xanthine dNTP
pyrophosphatase from Methanococcus jannaschii.";
Nucleic Acids Res. 29:3099-3107(2001).
[3]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
ATP ANALOG, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY,
COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
PubMed=10404228; DOI=10.1038/10745;
Hwang K.Y., Chung J.H., Kim S.-H., Han Y.S., Cho Y.;
"Structure-based identification of a novel NTPase from Methanococcus
jannaschii.";
Nat. Struct. Biol. 6:691-696(1999).
-!- FUNCTION: Pyrophosphatase that catalyzes the hydrolysis of
nucleoside triphosphates to their monophosphate derivatives, with
a high preference for the non-canonical purine nucleotides
xanthosine triphosphate (XTP), deoxyinosine triphosphate (dITP)
and ITP (PubMed:10404228, PubMed:11452035). Probably functions as
a house-cleaning enzyme that removes non-canonical purine
nucleotides from the nucleotide pool, thus preventing their
incorporation into DNA/RNA and avoiding chromosomal lesions
(PubMed:11452035). Shows very low activity on GTP or dGTP, both of
which are hydrolyzed more than 100-fold less efficiently than XTP,
and has nearly no activity toward the canonical nucleotides ATP,
CTP, and TTP, and toward 6-N-hydroxylaminopurine deoxynucleoside
triphosphate (dHAPTP) (PubMed:10404228, PubMed:11452035). Displays
neither endonuclease nor 3'-exonuclease activities
(PubMed:11452035). {ECO:0000269|PubMed:10404228,
ECO:0000269|PubMed:11452035}.
-!- CATALYTIC ACTIVITY: XTP + H(2)O = XMP + diphosphate.
{ECO:0000269|PubMed:10404228, ECO:0000269|PubMed:11452035}.
-!- CATALYTIC ACTIVITY: dITP + H(2)O = dIMP + diphosphate.
{ECO:0000269|PubMed:11452035}.
-!- CATALYTIC ACTIVITY: ITP + H(2)O = IMP + diphosphate.
{ECO:0000269|PubMed:10404228, ECO:0000269|PubMed:11452035}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:10404228,
ECO:0000269|PubMed:11452035};
Note=Binds 1 Mg(2+) ion per subunit (By similarity). Magnesium
ions are required for optimal activity, with Mn(2+), Zn(2+) and
Ni(2+) supporting <50% of the maximum rate (PubMed:11452035).
{ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000269|PubMed:10404228,
ECO:0000269|PubMed:11452035};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.10 mM for XTP (at pH 7.6 and 80 degrees Celsius)
{ECO:0000269|PubMed:10404228};
KM=0.15 mM for ITP (at pH 7.6 and 80 degrees Celsius)
{ECO:0000269|PubMed:10404228};
KM=1.11 mM for GTP (at pH 7.6 and 80 degrees Celsius)
{ECO:0000269|PubMed:10404228};
KM=1.13 mM for dGTP (at pH 7.6 and 80 degrees Celsius)
{ECO:0000269|PubMed:10404228};
KM=0.22 mM for XTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=0.25 mM for dITP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=0.24 mM for ITP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=2.12 mM for dGTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=1.94 mM for GTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=2.87 mM for 3'dGTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=2.78 mM for ddGTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=7.3 mM for dATP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=5.47 mM for dCTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=4.4 mM for dTTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=4.22 mM for dUTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=5.3 mM for 8-oxo-dGTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
KM=3.3 mM for dHAPTP (at pH 10.5 and 80 degrees Celsius)
{ECO:0000269|PubMed:11452035};
Note=kcat is 1009 sec(-1) with XTP as substrate. kcat is 911.7
sec(-1) with ITP as substrate. kcat is 97.6 sec(-1) with GTP as
substrate. kcat is 96.6 sec(-1) with dGTP as substrate (at pH
7.6 and 80 degrees Celsius) (PubMed:10404228). kcat is 176.4
sec(-1) with XTP as substrate. kcat is 152.4 sec(-1) with dITP
as substrate. kcat is 155.8 sec(-1) with ITP as substrate. kcat
is 9.3 sec(-1) with dGTP as substrate. kcat is 9.1 sec(-1) with
GTP as substrate. kcat is 8.2 sec(-1) with 3'dGTP as substrate.
kcat is 3.3 sec(-1) with ddGTP as substrate. kcat is 0.44 sec(-
1) with dATP as substrate. kcat is 0.44 sec(-1) with dCTP as
substrate. kcat is 1.8 sec(-1) with dTTP as substrate. kcat is
5.8 sec(-1) with dUTP as substrate. kcat is 2.4 sec(-1) with 8-
oxo-dGTP as substrate. kcat is 1.8 sec(-1) with dHAPTP as
substrate (at pH 10.5 and 80 degrees Celsius) (PubMed:11452035).
{ECO:0000269|PubMed:10404228, ECO:0000269|PubMed:11452035};
pH dependence:
Optimum pH is 10.5 with dITP as substrate. The reaction rates
under neutral conditions are <30% of maximum.
{ECO:0000269|PubMed:11452035};
Temperature dependence:
Optimum temperature is 80 degrees Celsius. At low temperature
(30 degrees Celsius), shows about 5-fold decrease in activity
compared to the maximum activity at 80 degrees Celsius. Is
highly thermostable. The half-life of the protein at 95 degrees
Celsius is about 200 minutes. {ECO:0000269|PubMed:11452035};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10404228}.
-!- SIMILARITY: Belongs to the HAM1 NTPase family. {ECO:0000255|HAMAP-
Rule:MF_01405}.
-!- SEQUENCE CAUTION:
Sequence=AAB98211.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; L77117; AAB98211.1; ALT_INIT; Genomic_DNA.
PIR; C64328; C64328.
RefSeq; WP_064496428.1; NC_000909.1.
PDB; 1B78; X-ray; 2.20 A; A/B=1-185.
PDB; 2MJP; X-ray; 2.20 A; A/B=1-185.
PDBsum; 1B78; -.
PDBsum; 2MJP; -.
SMR; Q57679; -.
STRING; 243232.MJ_0226; -.
EnsemblBacteria; AAB98211; AAB98211; MJ_0226.
GeneID; 1451077; -.
KEGG; mja:MJ_0226; -.
eggNOG; arCOG04184; Archaea.
eggNOG; COG0127; LUCA.
InParanoid; Q57679; -.
KO; K02428; -.
OrthoDB; POG093Z0DTZ; -.
BioCyc; MJAN243232:G1GKE-240-MONOMER; -.
BRENDA; 3.6.1.66; 3260.
BRENDA; 3.6.1.B14; 3260.
SABIO-RK; Q57679; -.
EvolutionaryTrace; Q57679; -.
Proteomes; UP000000805; Chromosome.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0035870; F:dITP diphosphatase activity; IDA:UniProtKB.
GO; GO:0036220; F:ITP diphosphatase activity; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0017111; F:nucleoside-triphosphatase activity; IEA:InterPro.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0036222; F:XTP diphosphatase activity; IDA:UniProtKB.
GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
GO; GO:0009146; P:purine nucleoside triphosphate catabolic process; IDA:UniProtKB.
CDD; cd00515; HAM1; 1.
Gene3D; 3.90.950.10; -; 1.
HAMAP; MF_01405; Non_canon_purine_NTPase; 1.
InterPro; IPR020922; dITP/XTP_pyrophosphatase.
InterPro; IPR002637; Ham1p-like.
InterPro; IPR029001; ITPase-like_fam.
PANTHER; PTHR11067; PTHR11067; 1.
Pfam; PF01725; Ham1p_like; 1.
SUPFAM; SSF52972; SSF52972; 1.
TIGRFAMs; TIGR00042; TIGR00042; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase; Magnesium; Metal-binding;
Nucleotide metabolism; Nucleotide-binding; Reference proteome.
CHAIN 1 185 dITP/XTP pyrophosphatase.
/FTId=PRO_0000178274.
REGION 7 12 Substrate binding. {ECO:0000255|HAMAP-
Rule:MF_01405}.
REGION 141 144 Substrate binding. {ECO:0000255|HAMAP-
Rule:MF_01405}.
REGION 169 170 Substrate binding. {ECO:0000244|PDB:2MJP,
ECO:0000255|HAMAP-Rule:MF_01405,
ECO:0000305|PubMed:10404228}.
ACT_SITE 65 65 Proton acceptor. {ECO:0000255|HAMAP-
Rule:MF_01405}.
METAL 37 37 Magnesium. {ECO:0000255|HAMAP-
Rule:MF_01405}.
METAL 65 65 Magnesium. {ECO:0000255|HAMAP-
Rule:MF_01405}.
BINDING 66 66 Substrate; via amide nitrogen.
{ECO:0000255|HAMAP-Rule:MF_01405}.
BINDING 164 164 Substrate. {ECO:0000255|HAMAP-
Rule:MF_01405}.
STRAND 3 6 {ECO:0000244|PDB:1B78}.
HELIX 10 19 {ECO:0000244|PDB:1B78}.
TURN 20 22 {ECO:0000244|PDB:1B78}.
STRAND 28 31 {ECO:0000244|PDB:1B78}.
STRAND 38 40 {ECO:0000244|PDB:1B78}.
HELIX 42 57 {ECO:0000244|PDB:1B78}.
STRAND 61 70 {ECO:0000244|PDB:1B78}.
HELIX 71 73 {ECO:0000244|PDB:1B78}.
HELIX 81 87 {ECO:0000244|PDB:1B78}.
HELIX 89 97 {ECO:0000244|PDB:1B78}.
STRAND 104 115 {ECO:0000244|PDB:1B78}.
STRAND 118 130 {ECO:0000244|PDB:1B78}.
HELIX 142 145 {ECO:0000244|PDB:1B78}.
STRAND 146 149 {ECO:0000244|PDB:1B78}.
HELIX 156 158 {ECO:0000244|PDB:1B78}.
HELIX 161 164 {ECO:0000244|PDB:1B78}.
TURN 165 167 {ECO:0000244|PDB:1B78}.
HELIX 169 182 {ECO:0000244|PDB:1B78}.
SEQUENCE 185 AA; 21273 MW; 97EC2DA5C0D21D67 CRC64;
MKIYFATGNP NKIKEANIIL KDLKDVEIEQ IKISYPEIQG TLEEVAEFGA KWVYNILKKP
VIVEDSGFFV EALNGFPGTY SKFVQETIGN EGILKLLEGK DNRNAYFKTV IGYCDENGVR
LFKGIVKGRV SEEIRSKGYG FAYDSIFIPE EEERTFAEMT TEEKSQISHR KKAFEEFKKF
LLDRI


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