NDX1_THETH
ID NDX1_THETH Reviewed; 126 AA.
AC Q75UV1; F6DFL8;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=Diadenosine hexaphosphate hydrolase {ECO:0000303|PubMed:15024014};
DE Short=Ap6A hydrolase {ECO:0000303|PubMed:15024014};
DE EC=3.6.1.61 {ECO:0000269|PubMed:15024014};
DE AltName: Full=ATP-generating (di)nucleotide polyphosphate hydrolase {ECO:0000303|PubMed:15024014};
DE AltName: Full=ATP-generating Ap6A hydrolase {ECO:0000303|PubMed:15024014};
DE AltName: Full=Nudix protein {ECO:0000303|PubMed:15024014};
GN Name=ndx1 {ECO:0000303|PubMed:15024014};
OS Thermus thermophilus.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-9, FUNCTION,
RP CATALYTIC ACTIVITY, MUTAGENESIS OF TRP-26; GLU-46; GLU-49 AND GLU-50,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP COFACTOR, AND SUBUNIT.
RC STRAIN=HB8;
RX PubMed=15024014; DOI=10.1074/jbc.m312018200;
RA Iwai T., Kuramitsu S., Masui R.;
RT "The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine
RT hexaphosphate hydrolase with a novel activity.";
RL J. Biol. Chem. 279:21732-21739(2004).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS
RP AND MAGNESIUM ION, AND SUBUNIT.
RA Iwai T., Nakagawa N., Kuramitsu S., Masui R.;
RT "Crystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in
RT binary complex with diadenosine hexaphosphate.";
RL Submitted (MAR-2004) to the PDB data bank.
CC -!- FUNCTION: Specifically hydrolyzes (di)adenosine polyphosphates but not
CC ATP or diadenosine triphosphate, generating ATP as the product.
CC Diadenosine hexaphosphate (Ap6A) is the preferred substrate and
CC hydrolysis yields 2 ATP. It is the only enzyme that symmetrically
CC hydrolyzes Ap6A. It also hydrolyzes diadenosine pentaphosphate (Ap5A),
CC diadenosine tetraphosphate (Ap4A) and adenosine tetraphosphate (p4A).
CC {ECO:0000269|PubMed:15024014}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(6)-bis(5'-adenosyl) hexaphosphate = 2 ATP + 2
CC H(+); Xref=Rhea:RHEA:32043, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:63740; EC=3.6.1.61;
CC Evidence={ECO:0000269|PubMed:15024014};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(5)-bis(5'-adenosyl) pentaphosphate = ADP + ATP +
CC 2 H(+); Xref=Rhea:RHEA:30527, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:62041, ChEBI:CHEBI:456216;
CC EC=3.6.1.61; Evidence={ECO:0000269|PubMed:15024014};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + P(1),P(4)-bis(5'-adenosyl) tetraphosphate = AMP + ATP +
CC 2 H(+); Xref=Rhea:RHEA:32039, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58141, ChEBI:CHEBI:456215;
CC EC=3.6.1.61; Evidence={ECO:0000269|PubMed:15024014};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15024014};
CC Note=Also able to use Mn(2+) and Zn(2+), but the activity is less than
CC that obtained with Mg(2+) ions. {ECO:0000269|PubMed:15024014};
CC -!- ACTIVITY REGULATION: Strongly inhibited by fluoride ions.
CC {ECO:0000269|PubMed:15024014}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1 uM for p4A (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:15024014};
CC KM=1.1 uM for Ap4A (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:15024014};
CC KM=1.1 uM for Ap5A (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:15024014};
CC KM=1.4 uM for Ap6A (at 25 degrees Celsius)
CC {ECO:0000269|PubMed:15024014};
CC KM=1.4 uM for diguanosine pentaphosphate (Gp5G) (at 25 degrees
CC Celsius) {ECO:0000269|PubMed:15024014};
CC KM=9.3 uM for diguanosine tetraphosphate (Gp4G) (at 25 degrees
CC Celsius) {ECO:0000269|PubMed:15024014};
CC Note=kcat is 4.1 sec(-1) with Ap6A (at 25 degrees Celsius). kcat is
CC 1.4 sec(-1) with p4A (at 25 degrees Celsius). kcat is 0.52 sec(-1)
CC with Ap5A (at 25 degrees Celsius). kcat is 0.27 sec(-1) with Ap4A (at
CC 25 degrees Celsius).;
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:15024014};
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius. Ndx1 is stable up to 95
CC degrees Celsius at pH 7.5. {ECO:0000269|PubMed:15024014};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:15024014, ECO:0000305|Ref.2}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; AB125632; BAD18071.1; -; Genomic_DNA.
DR RefSeq; WP_011228981.1; NZ_AP019801.1.
DR RefSeq; YP_145146.1; NC_006461.1.
DR PDB; 1VC8; X-ray; 2.00 A; A/B=1-126.
DR PDB; 1VC9; X-ray; 2.30 A; A/B=1-126.
DR PDB; 1VCD; X-ray; 1.70 A; A/B=1-126.
DR PDBsum; 1VC8; -.
DR PDBsum; 1VC9; -.
DR PDBsum; 1VCD; -.
DR AlphaFoldDB; Q75UV1; -.
DR SMR; Q75UV1; -.
DR DrugBank; DB02738; Adenosine-5'-Pentaphosphate.
DR GeneID; 3169127; -.
DR OMA; KITWYLM; -.
DR BRENDA; 3.6.1.61; 2305.
DR EvolutionaryTrace; Q75UV1; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016818; F:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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 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; ATP-binding; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding; Nucleotide-binding.
FT CHAIN 1..126
FT /note="Diadenosine hexaphosphate hydrolase"
FT /id="PRO_0000422740"
FT DOMAIN 1..121
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 31..52
FT /note="Nudix box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT BINDING 21..23
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 30..32
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 46
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 50
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:15024014"
FT BINDING 66..68
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 74
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.2"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.2"
FT MUTAGEN 26
FT /note="W->A: Strong decrease of the affinity for Ap6A."
FT /evidence="ECO:0000269|PubMed:15024014"
FT MUTAGEN 46
FT /note="E->Q: Strong decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15024014"
FT MUTAGEN 49
FT /note="E->Q: Very little effect on hydrolase activity."
FT /evidence="ECO:0000269|PubMed:15024014"
FT MUTAGEN 50
FT /note="E->Q: Strong decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15024014"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:1VCD"
FT STRAND 16..20
FT /evidence="ECO:0007829|PDB:1VCD"
FT HELIX 39..51
FT /evidence="ECO:0007829|PDB:1VCD"
FT STRAND 54..67
FT /evidence="ECO:0007829|PDB:1VCD"
FT STRAND 73..85
FT /evidence="ECO:0007829|PDB:1VCD"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:1VCD"
FT HELIX 101..107
FT /evidence="ECO:0007829|PDB:1VCD"
FT HELIX 111..123
FT /evidence="ECO:0007829|PDB:1VCD"
SQ SEQUENCE 126 AA; 14170 MW; DD5E2B3ECC839F4B CRC64;
MELGAGGVVF NAKREVLLLR DRMGFWVFPK GHPEPGESLE EAAVREVWEE TGVRAEVLLP
LYPTRYVNPK GVEREVHWFL MRGEGAPRLE EGMTGAGWFS PEEARALLAF PEDLGLLEVA
LERLPL
