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Protein

Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]

Gene

ndx-4

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Asymmetrically hydrolyzes Ap4A to yield AMP and ATP.1 Publication

Catalytic activityi

P1,P(4)-bis(5'-adenosyl) tetraphosphate + H2O = ATP + AMP.

Cofactori

Mg2+1 Publication, Co2+1 Publication, Mn2+1 Publication, Zn2+1 Publication, Ca2+1 PublicationNote: Divalent metal ions. Mg2+, Co2+, Mn2+, Zn2+ or Ca2+.1 Publication

GO - Molecular functioni

  • 5-phosphoribosyl 1-pyrophosphate pyrophosphatase activity Source: WormBase
  • ATP binding Source: UniProtKB-KW
  • bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity Source: UniProtKB

GO - Biological processi

  • ADP biosynthetic process Source: WormBase
  • AMP biosynthetic process Source: WormBase
  • apoptotic process Source: UniProtKB
  • ATP biosynthetic process Source: WormBase
  • diadenosine tetraphosphate catabolic process Source: WormBase
  • ribose phosphate metabolic process Source: WormBase
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

ATP-binding, Calcium, Cobalt, Magnesium, Manganese, Nucleotide-binding, Zinc

Enzyme and pathway databases

BRENDAi3.6.1.17. 1045.
ReactomeiR-CEL-3299685. Detoxification of Reactive Oxygen Species.
SABIO-RKQ9U2M7.

Names & Taxonomyi

Protein namesi
Recommended name:
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] (EC:3.6.1.-)
Alternative name(s):
Diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase
Short name:
Ap4A hydrolase
Short name:
Ap4Aase
Short name:
Diadenosine tetraphosphatase
Nudix hydrolase 4
Gene namesi
Name:ndx-4
ORF Names:Y37H9A.6
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome I

Organism-specific databases

WormBaseiY37H9A.6; CE20230; WBGene00003581; ndx-4.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi27 – 271Y → A: No Effect on substrate binding or catalytic activity. 1 Publication
Mutagenesisi27 – 271Y → D: Slight increase in substrate binding and no effect on catalytic activity. 1 Publication
Mutagenesisi31 – 311H → A: Increases substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi31 – 311H → V: Increases substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi36 – 361K → M: No effect on substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi38 – 381H → G: Slight decrease in substrate binding and slight increase in catalytic activity. 1 Publication
Mutagenesisi38 – 381H → K: Slight decrease in substrate binding and slight increase in catalytic activity. 1 Publication
Mutagenesisi52 – 521E → Q: No effect on substrate binding and strongly reduces catalytic activity. 1 Publication
Mutagenesisi56 – 561E → Q: No effect on substrate binding and strongly reduces catalytic activity. 1 Publication
Mutagenesisi76 – 761Y → A: Increases substrate binding and slightly reduces catalytic activity. Reduces catalytic activity; when associated with A-121. 1 Publication
Mutagenesisi79 – 791K → M: Slight increase in substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi81 – 811K → M: Slight increase in substrate binding and enzyme activity. 1 Publication
Mutagenesisi83 – 831K → M: Increases substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi103 – 1031E → Q: No effect on substrate binding and reduces catalytic activity. 1 Publication
Mutagenesisi121 – 1211Y → A: Increases substrate binding and slightly reduces catalytic activity. Reduces catalytic activity; when associated with A-76. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 138138Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]PRO_0000057106Add
BLAST

Proteomic databases

EPDiQ9U2M7.
PaxDbiQ9U2M7.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi54272. 1 interaction.
DIPiDIP-24985N.
MINTiMINT-1125473.
STRINGi6239.Y37H9A.6.1.

Structurei

Secondary structure

1
138
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 1412Combined sources
Beta strandi17 – 2711Combined sources
Beta strandi32 – 387Combined sources
Helixi45 – 5713Combined sources
Helixi61 – 633Combined sources
Beta strandi64 – 7815Combined sources
Beta strandi81 – 9212Combined sources
Beta strandi104 – 1107Combined sources
Helixi112 – 1198Combined sources
Helixi122 – 13716Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KT9X-ray1.98A1-138[»]
1KTGX-ray1.80A/B1-138[»]
ProteinModelPortaliQ9U2M7.
SMRiQ9U2M7. Positions 2-138.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9U2M7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 132132Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi37 – 5822Nudix boxAdd
BLAST

Domaini

Mutagenesis suggests that interactions with P1- and P4-phosphate are minimum indicating the enzyme may have a wide substrate range.

Sequence similaritiesi

Belongs to the Nudix hydrolase family.Curated
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2839. Eukaryota.
COG0494. LUCA.
GeneTreeiENSGT00390000002416.
HOGENOMiHOG000261976.
InParanoidiQ9U2M7.
KOiK01518.
OMAiHHWSPPK.
PhylomeDBiQ9U2M7.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR003565. Tetra_PHTase.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR01405. TETRPHPHTASE.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9U2M7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVVKAAGLVI YRKLAGKIEF LLLQASYPPH HWTPPKGHVD PGEDEWQAAI
60 70 80 90 100
RETKEEANIT KEQLTIHEDC HETLFYEAKG KPKSVKYWLA KLNNPDDVQL
110 120 130
SHEHQNWKWC ELEDAIKIAD YAEMGSLLRK FSAFLAGF
Length:138
Mass (Da):15,889
Last modified:May 1, 2000 - v1
Checksum:i5C123085602CE5E5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL032625 Genomic DNA. Translation: CAB63351.1.
RefSeqiNP_493413.1. NM_061012.4.
UniGeneiCel.16496.

Genome annotation databases

EnsemblMetazoaiY37H9A.6; Y37H9A.6; WBGene00003581.
GeneIDi189639.
KEGGicel:CELE_Y37H9A.6.
UCSCiY37H9A.6.2. c. elegans.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL032625 Genomic DNA. Translation: CAB63351.1.
RefSeqiNP_493413.1. NM_061012.4.
UniGeneiCel.16496.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KT9X-ray1.98A1-138[»]
1KTGX-ray1.80A/B1-138[»]
ProteinModelPortaliQ9U2M7.
SMRiQ9U2M7. Positions 2-138.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi54272. 1 interaction.
DIPiDIP-24985N.
MINTiMINT-1125473.
STRINGi6239.Y37H9A.6.1.

Proteomic databases

EPDiQ9U2M7.
PaxDbiQ9U2M7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiY37H9A.6; Y37H9A.6; WBGene00003581.
GeneIDi189639.
KEGGicel:CELE_Y37H9A.6.
UCSCiY37H9A.6.2. c. elegans.

Organism-specific databases

CTDi189639.
WormBaseiY37H9A.6; CE20230; WBGene00003581; ndx-4.

Phylogenomic databases

eggNOGiKOG2839. Eukaryota.
COG0494. LUCA.
GeneTreeiENSGT00390000002416.
HOGENOMiHOG000261976.
InParanoidiQ9U2M7.
KOiK01518.
OMAiHHWSPPK.
PhylomeDBiQ9U2M7.

Enzyme and pathway databases

BRENDAi3.6.1.17. 1045.
ReactomeiR-CEL-3299685. Detoxification of Reactive Oxygen Species.
SABIO-RKQ9U2M7.

Miscellaneous databases

EvolutionaryTraceiQ9U2M7.
NextBioi943106.
PROiQ9U2M7.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR003565. Tetra_PHTase.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR01405. TETRPHPHTASE.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, characterisation and crystallisation of a diadenosine 5',5''-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans."
    Abdelghany H.M., Gasmi L., Cartwright J.L., Bailey S., Rafferty J.B., McLennan A.G.
    Biochim. Biophys. Acta 1550:27-36(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), FUNCTION, COFACTOR.
    Strain: Bristol N2.
  2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Bristol N2.
  3. "Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis."
    Abdelghany H.M., Bailey S., Blackburn G.M., Rafferty J.B., McLennan A.G.
    J. Biol. Chem. 278:4435-4439(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.
    Strain: Bristol N2.
  4. "The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms."
    Bailey S., Sedelnikova S.E., Blackburn G.M., Abdelghany H.M., Baker P.J., McLennan A.G., Rafferty J.B.
    Structure 10:589-600(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SUBUNIT.
  5. "Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA."
    Bailey S., Sedelnikova S.E., Blackburn G.M., Abdelghany H.M., McLennan A.G., Rafferty J.B.
    Acta Crystallogr. D 58:526-528(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Entry informationi

Entry nameiAP4A_CAEEL
AccessioniPrimary (citable) accession number: Q9U2M7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: May 1, 2000
Last modified: May 11, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.