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Protein

Non-canonical purine NTP phosphatase

Gene

yjjX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions. ITP is the best substrate, followed by XTP, GDP or dITP. Also implicated in the resistance against the thiamine metabolism inhibitors bacimethrin and CF3-HMP.1 Publication

Catalytic activityi

A nucleoside triphosphate + H2O = a nucleoside diphosphate + monophosphate.

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: Binds 1 divalent cation per subunit. Activity is maximal in the presence of Mg2+, while Mn2+ decreases the activity by 20%.1 Publication

Enzyme regulationi

Competitively inhibited by ATP, GTP and TTP.

Kineticsi

  1. KM=0.5 mM for ITP1 Publication
  2. KM=0.58 mM for GDP1 Publication
  3. KM=0.91 mM for magnesium ions1 Publication
  4. KM=1.17 mM for XTP1 Publication
  5. KM=1.24 mM for GTP1 Publication
  6. KM=1.39 mM for manganese ions1 Publication
  7. KM=2.44 mM for zinc ions1 Publication
  8. KM=4.51 mM for dITP1 Publication
  1. Vmax=67 µmol/min/mg enzyme with GTP as substrate1 Publication
  2. Vmax=358 µmol/min/mg enzyme with GDP as substrate1 Publication
  3. Vmax=439 µmol/min/mg enzyme with ITP as substrate and zinc ions as cofactor (ar 15 degrees Celsius and at pH 6.75)1 Publication
  4. Vmax=571 µmol/min/mg enzyme with ITP as substrate and manganese ions as cofactor (ar 15 degrees Celsius and at pH 6.75)1 Publication
  5. Vmax=1264 µmol/min/mg enzyme with ITP as substrate and magnesium ions as cofactor (ar 15 degrees Celsius and at pH 6.75)1 Publication
  6. Vmax=1720 µmol/min/mg enzyme with ITP as substrate1 Publication
  7. Vmax=1849 µmol/min/mg enzyme with dITP as substrate1 Publication
  8. Vmax=7876 µmol/min/mg enzyme with XTP as substrate1 Publication

pH dependencei

Optimum pH is 6.75.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi38Manganese or magnesiumBy similarity1
Metal bindingi68Manganese or magnesiumBy similarity1

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • nucleoside-triphosphatase activity Source: EcoCyc
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antibiotic resistance, Nucleotide metabolism

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12600-MONOMER.
ECOL316407:JW5801-MONOMER.
MetaCyc:EG12600-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Non-canonical purine NTP phosphatase (EC:3.6.1.-)
Alternative name(s):
Inosine triphosphatase
Short name:
ITPase
Non-standard purine NTP phosphatase
Nucleoside-triphosphate phosphatase
Short name:
NTPase
Xanthosine triphosphatase
Short name:
XTPase
Gene namesi
Name:yjjX
Ordered Locus Names:b4394, JW5801
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12600. yjjX.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001563371 – 170Non-canonical purine NTP phosphataseAdd BLAST170

Proteomic databases

PaxDbiP39411.
PRIDEiP39411.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4262781. 5 interactors.
DIPiDIP-12663N.
STRINGi511145.b4394.

Structurei

Secondary structure

1170
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Helixi11 – 25Combined sources15
Beta strandi30 – 34Combined sources5
Helixi48 – 65Combined sources18
Beta strandi69 – 79Combined sources11
Beta strandi81 – 94Combined sources14
Beta strandi96 – 100Combined sources5
Helixi108 – 114Combined sources7
Turni115 – 117Combined sources3
Helixi120 – 125Combined sources6
Helixi133 – 135Combined sources3
Helixi138 – 143Combined sources6
Turni144 – 146Combined sources3
Helixi150 – 161Combined sources12
Helixi163 – 166Combined sources4
Helixi168 – 170Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1U5WX-ray2.30A/B/C/D/E/F/G/H1-170[»]
ProteinModelPortaliP39411.
SMRiP39411.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39411.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 13Substrate binding6
Regioni68 – 69Substrate bindingBy similarity2

Sequence similaritiesi

Belongs to the YjjX NTPase family.Curated

Phylogenomic databases

eggNOGiENOG4108K16. Bacteria.
COG1986. LUCA.
HOGENOMiHOG000098033.
InParanoidiP39411.
OMAiADQPMTE.
PhylomeDBiP39411.

Family and domain databases

Gene3Di3.90.950.10. 1 hit.
HAMAPiMF_00648. Non_canon_purine_NTPase_YjjX. 1 hit.
InterProiIPR029001. ITPase-like_fam.
IPR002786. Non_canon_purine_NTPase.
IPR026533. NTPase/PRRC1.
[Graphical view]
PfamiPF01931. NTPase_I-T. 1 hit.
[Graphical view]
SUPFAMiSSF52972. SSF52972. 1 hit.
TIGRFAMsiTIGR00258. TIGR00258. 1 hit.

Sequencei

Sequence statusi: Complete.

P39411-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHQVVCATTN PAKIQAILQA FHEIFGEGSC HIASVAVESG VPEQPFGSEE
60 70 80 90 100
TRAGARNRVA NARRLLPEAD FWVAIEAGID GDSTFSWVVI ENASQRGEAR
110 120 130 140 150
SATLPLPAVI LEKVREGEAL GPVMSRYTGI DEIGRKEGAI GVFTAGKLTR
160 170
ASVYHQAVIL ALSPFHNAVY
Length:170
Mass (Da):18,213
Last modified:August 29, 2001 - v2
Checksum:i60F87FEB6344E597
GO

Sequence cautioni

The sequence AAA97290 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti146 – 152GKLTRAS → ETHSRH in AAA72135 (PubMed:7841459).Curated7

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14003 Genomic DNA. Translation: AAA97290.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77347.2.
AP009048 Genomic DNA. Translation: BAE78383.1.
J01715 Genomic DNA. No translation available.
L13768 Genomic DNA. Translation: AAA72135.1.
PIRiS56618.
RefSeqiNP_418811.2. NC_000913.3.
WP_001338221.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77347; AAC77347; b4394.
BAE78383; BAE78383; BAE78383.
GeneIDi948919.
KEGGiecj:JW5801.
eco:b4394.
PATRICi32124406. VBIEscCol129921_4543.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14003 Genomic DNA. Translation: AAA97290.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77347.2.
AP009048 Genomic DNA. Translation: BAE78383.1.
J01715 Genomic DNA. No translation available.
L13768 Genomic DNA. Translation: AAA72135.1.
PIRiS56618.
RefSeqiNP_418811.2. NC_000913.3.
WP_001338221.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1U5WX-ray2.30A/B/C/D/E/F/G/H1-170[»]
ProteinModelPortaliP39411.
SMRiP39411.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262781. 5 interactors.
DIPiDIP-12663N.
STRINGi511145.b4394.

Proteomic databases

PaxDbiP39411.
PRIDEiP39411.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77347; AAC77347; b4394.
BAE78383; BAE78383; BAE78383.
GeneIDi948919.
KEGGiecj:JW5801.
eco:b4394.
PATRICi32124406. VBIEscCol129921_4543.

Organism-specific databases

EchoBASEiEB2485.
EcoGeneiEG12600. yjjX.

Phylogenomic databases

eggNOGiENOG4108K16. Bacteria.
COG1986. LUCA.
HOGENOMiHOG000098033.
InParanoidiP39411.
OMAiADQPMTE.
PhylomeDBiP39411.

Enzyme and pathway databases

BioCyciEcoCyc:EG12600-MONOMER.
ECOL316407:JW5801-MONOMER.
MetaCyc:EG12600-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39411.
PROiP39411.

Family and domain databases

Gene3Di3.90.950.10. 1 hit.
HAMAPiMF_00648. Non_canon_purine_NTPase_YjjX. 1 hit.
InterProiIPR029001. ITPase-like_fam.
IPR002786. Non_canon_purine_NTPase.
IPR026533. NTPase/PRRC1.
[Graphical view]
PfamiPF01931. NTPase_I-T. 1 hit.
[Graphical view]
SUPFAMiSSF52972. SSF52972. 1 hit.
TIGRFAMsiTIGR00258. TIGR00258. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNCPP_ECOLI
AccessioniPrimary (citable) accession number: P39411
Secondary accession number(s): Q2M5S3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: August 29, 2001
Last modified: November 2, 2016
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

PubMed:7841459 sequence was originally thought to originate from S.typhimurium, but seems to come from an unknown E.coli strain.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.