Nucleoside-triphosphatase rdgB - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P52061 (RDGB_ECOLI)

Last modified June 16, 2009. Version 67. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Nucleoside-triphosphatase rdgB
    EC=3.6.1.15
Alternative name(s):
    Nucleoside triphosphate phosphohydrolase
      Short name=NTPase

Gene names

Name:	rdgB
Synonyms:	yggV
Ordered Locus Names:	b2954, JW2921

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	197 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Hydrolyzes O6 atom-containing purine bases deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) to nucleotide monophosphate and pyrophosphate. Probably excludes non-standard purines from DNA precursor pool, preventing thus incorporation into DNA and avoiding chromosomal lesions. Ref.4
Catalytic activity	NTP + H₂O = NDP + phosphate. Ref.3
Cofactor	Divalent cations. Maximum activity is obtained with magnesium. Activity with manganese and nickel makes up 60-75% of the maximum rate. Ref.3
Subunit structure	Homodimer. Ref.3
Miscellaneous	Activity toward dATP, dCTP and dTTP is less than 1% of the rate of XTP hydrolysis. Activity toward dGTP and dUTP is 10-12% lower than activity toward XTP. Modified or damaged nucleotides such as 6-chloropurine deoxyribose triphosphate, 8-Br-dGTP, 5-Br-dCTP, 5-Br-dUTP, 7-deaza-dGTP, 7-methyl-GTP, N6-etheno-ATP, NAD, NADH, FAD, ADP-ribose, UPD-glucose, AppA and ApppA are not hydrolyzed. HAMAP MF_01405
Sequence similarities	Belongs to the HAM1 NTPase family.
biophysicochemical properties	Kinetic parameters: Vmax values are similar for XTP, dITP and ITP. K_M=0.33 mM for XTP HAMAP MF_01405 K_M=0.36 mM for dITP K_M=0.41 mM for ITP K_M=16.5 µM for dHAPTP pH dependence: Optimum pH is 10-10.5.

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Ontologies

Keywords
Ligand	Magnesium Manganese Nickel
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-triphosphatase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 197

197

Nucleoside-triphosphatase rdgB HAMAP MF_01405

PRO_0000178164

Secondary structure

197

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P52061-1 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 74E82A59B1A9E294
Show »

FASTA

197

21,039

        10         20         30         40         50         60 
MQKVVLATGN VGKVRELASL LSDFGLDIVA QTDLGVDSAE ETGLTFIENA ILKARHAAKV 

        70         80         90        100        110        120 
TALPAIADDS GLAVDVLGGA PGIYSARYSG EDATDQKNLQ KLLETMKDVP DDQRQARFHC 

       130        140        150        160        170        180 
VLVYLRHAED PTPLVCHGSW PGVITREPAG TGGFGYDPIF FVPSEGKTAA ELTREEKSAI 

       190 
SHRGQALKLL LDALRNG

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"Identification of the dITP- and XTP-hydrolyzing protein from Escherichia coli." Chung J.H., Park H.-Y., Lee J.H., Jang Y. J. Biochem. Mol. Biol. 35:403-408(2002) [PubMed: 12297000] [Abstract] Cited for: CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
[4]	"Substrate specificity of RdgB protein, a deoxyribonucleoside triphosphate pyrophosphohydrolase." Burgis N.E., Cunningham R.P. J. Biol. Chem. 282:3531-3538(2007) [PubMed: 17090528] [Abstract] Cited for: SUBSTRATE SPECIFICITY, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
[5]	"Putative ribosomal protein." Midwest center for structural genomics (MCSG) Submitted (JAN-2005) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS).
+	Additional computationally mapped references.

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Cross-references

Sequence databases

U28377 Genomic DNA. Translation: AAA69121.1.
U00096 Genomic DNA. Translation: AAC75991.1.
AP009048 Genomic DNA. Translation: BAE77017.1.

PIR

A65081.

RefSeq

AP_003511.1.
NP_417429.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K7K	X-ray	1.50	A	1-197	[»]
2PYU	X-ray	2.02	A	1-197	[»]
2Q16	X-ray	1.95	A/B	1-197	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:12197N.

Genome annotation databases

GeneID

947429.

GenomeReviews

Gene locus JW2921 in contig AP009048_GR.
Gene locus b2954 in contig U00096_GR.

KEGG

ecj:JW2921.
eco:b2954.

Organism-specific databases

EchoBASE

EB2807.

EcoGene

EG12982. rdgB.

CMR

Search...

Phylogenomic databases

HOGENOM

P52061.

OMA

P52061. VYTADWA.

Enzyme and pathway databases

BioCyc

EcoCyc:G7530-MON.
MetaCyc:G7530-MON.

Family and domain databases

HAMAP

MF_01405.
[Tree]

InterPro

IPR002637. Ham1p-like.
[Graphical view]

PANTHER

PTHR11067. Ham1p_like. 1 hit.

Pfam

PF01725. Ham1p_like. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00042. Ham1p_like. 1 hit.

ProtoNet

Search...

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Entry information

Entry name

RDGB_ECOLI

Accession

Primary (citable) accession number: P52061
Secondary accession number(s): Q2M9N9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	June 16, 2009
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families