Q93K97 (ADPP_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ADP-ribose pyrophosphatase
EC=3.6.1.13

Alternative name(s):
ADP-ribose diphosphatase
ADP-ribose phosphohydrolase
Short name=ASPPase
Adenosine diphosphoribose pyrophosphatase
Short name=ADPR-PPase

Gene names

Name:	nudF
Synonyms:	aspP, yqiE, yzzG
Ordered Locus Names:	b3034, JW3002

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	209 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts on ADP-mannose and ADP-glucose as well as ADP-ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process. Ref.1
Catalytic activity	ADP-ribose + H2O = AMP + D-ribose 5-phosphate. Ref.6
Cofactor	Binds 3 magnesium ions per subunit. Ref.6 Ref.7
Enzyme regulation	Inhibited by phosphorylated compounds such as AMP, ADP, ATP, 3-phosphoglyceric acid and PPi. Not inhibited by orthophosphate. Activity is high in cells grown in low glucose concentrations and decreases dramatically as glucose concentration increases.
Subunit structure	Homodimer. Ref.6
Sequence similarities	Belongs to the Nudix hydrolase family. NudF subfamily. Contains 1 nudix hydrolase domain.

Ontologies

Keywords
Ligand	Magnesium Manganese Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
Molecular function	ADP-ribose diphosphatase activity Inferred from direct assay Ref.5. Source: EcoCyc magnesium ion binding Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 209

209

ADP-ribose pyrophosphatase

PRO_0000057042

Regions

Domain

55 – 193

139

Nudix hydrolase

Region

28 – 29

2

Substrate binding

Region

51 – 52

2

Substrate binding; shared with dimeric partner

Region

133 – 135

3

Substrate binding; shared with dimeric partner

Motif

97 – 118

22

Nudix box

Sites

Active site

162

1

Proton acceptor Probable

Metal binding

96

1

Magnesium 1; via carbonyl oxygen

Metal binding

112

1

Magnesium 2

Metal binding

112

1

Magnesium 3

Metal binding

116

1

Magnesium 1

Metal binding

116

1

Magnesium 3

Metal binding

164

1

Magnesium 3

Binding site

56

1

Substrate

Binding site

79

1

Substrate

Binding site

98

1

Substrate; via amide nitrogen

Binding site

139

1

Substrate

Experimental info

Sequence conflict

2

1

L → V in CAC44036. Ref.1

Sequence conflict

6

1

N → S in CAC44036. Ref.1

Secondary structure

1

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209

Helix Strand Turn

Details...

Beta strand

8 – 10

3

Helix

13 – 15

3

Beta strand

16 – 39

24

Beta strand

49 – 55

7

Beta strand

59 – 66

8

Turn

67 – 70

4

Beta strand

71 – 78

8

Helix

80 – 85

6

Beta strand

89 – 93

5

Beta strand

95 – 98

4

Helix

105 – 117

13

Beta strand

124 – 132

9

Turn

134 – 136

3

Beta strand

140 – 147

8

Helix

150 – 152

3

Beta strand

167 – 172

6

Helix

173 – 181

9

Helix

188 – 207

20

Sequences

	Sequence		Length	Mass (Da)
	Q93K97 [UniParc]. Last modified April 13, 2004. Version 2. Checksum: 2CF77EA9D63B9615	FASTA	209	23,667
	10 20 30 40 50 60 MLKPDNLPVT FGKNDVEIIA RETLYRGFFS LDLYRFRHRL FNGQMSHEVR REIFERGHAA 70 80 90 100 110 120 VLLPFDPVRD EVVLIEQIRI AAYDTSETPW LLEMVAGMIE EGESVEDVAR REAIEEAGLI 130 140 150 160 170 180 VKRTKPVLSF LASPGGTSER SSIMVGEVDA TTASGIHGLA DENEDIRVHV VSREQAYQWV 190 200 EEGKIDNAAS VIALQWLQLH HQALKNEWA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis in Escherichia coli." Moreno-Bruna B., Baroja-Fernandez E., Munoz F.J., Bastarrica-Berasategui A., Zandueta-Criado A., Rodriguez-Lopez M., Lasa I., Akazawa T., Pozueta-Romero J. Proc. Natl. Acad. Sci. U.S.A. 98:8128-8132(2001) [PubMed: 11416161] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION. Strain: BL21.
[2]	"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.
[3]	"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.
[4]	"Identification of the cpdA gene encoding cyclic 3',5'-adenosine monophosphate phosphodiesterase in Escherichia coli." Imamura R., Yamanaka K., Ogura T., Hiraga S., Fujita N., Ishihama A., Niki H. J. Biol. Chem. 271:25423-25429(1996) [PubMed: 8810311] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 98-209. Strain: K12.
[5]	"Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance." Dunn C.A., O'Handley S.F., Frick D.N., Bessman M.J. J. Biol. Chem. 274:32318-32324(1999) [PubMed: 10542272] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / MG1655 / ATCC 47076.
[6]	"The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family." Gabelli S.B., Bianchet M.A., Bessman M.J., Amzel L.M. Nat. Struct. Biol. 8:467-472(2001) [PubMed: 11323725] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOPROTEIN AND COMPLEXES WITH ADP-RIBOSE AND GADOLINIUM IONS, COFACTOR, CATALYTIC ACTIVITY, SUBUNIT.
[7]	"Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase." Gabelli S.B., Bianchet M.A., Ohnishi Y., Ichikawa Y., Bessman M.J., Amzel L.M. Biochemistry 41:9279-9285(2002) [PubMed: 12135348] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS), IN COMPLEX WITH AMPCPR AND MAGNESIUM IONS, COFACTOR, CATALYTIC MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ298136 Genomic DNA. Translation: CAC44036.1.
U28377 Genomic DNA. Translation: AAA69202.1.
U00096 Genomic DNA. Translation: AAC76070.1.
AP009048 Genomic DNA. Translation: BAE77090.1.
D16557 Genomic DNA. No translation available.

PIR

H65090.

RefSeq

NP_417506.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G0S	X-ray	1.90	A/B	1-209	[»]
1G9Q	X-ray	2.30	A/B	1-209	[»]
1GA7	X-ray	2.71	A/B	1-209	[»]
1KHZ	X-ray	2.04	A/B	1-209	[»]
1VIQ	X-ray	2.40	A/B/C	2-209	[»]

ProteinModelPortal

Q93K97.

SMR

Q93K97. Positions 8-209.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36214N.

IntAct

Q93K97. 7 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003243; EBESCP00000003243; EBESCG00000002662.
EBESCT00000016438; EBESCP00000015729; EBESCG00000015498.

GeneID

947519.

GenomeReviews

Gene locus JW3002 in contig AP009048_GR.
Gene locus b3034 in contig U00096_GR.

KEGG

ecj:JW3002.
eco:b3034.

PATRIC

32121478. VBIEscCol129921_3126.

Organism-specific databases

EcoGene

EG12184. nudF.

Phylogenomic databases

eggNOG

COG0494.

GeneTree

EBGT00050000011193.

HOGENOM

HBG692398.

OMA

LQWLELN.

PhylomeDB

Q93K97.

ProtClustDB

PRK10729.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12633-MONOMER.
MetaCyc:EG12633-MONOMER.

Gene expression databases

Genevestigator

Q93K97.

Family and domain databases

InterPro

IPR004385. NDP_pyrophosphatase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]

Gene3D

G3DSA:3.90.79.10. NUDIX_hydrolase. 1 hit.

KO

K01515.

Pfam

PF00293. NUDIX. 1 hit.
[Graphical view]

SUPFAM

SSF55811. NUDIX_hydrolase. 1 hit.

TIGRFAMs

TIGR00052. TIGR00052. 1 hit.

PROSITE

PS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

ADPP_ECOLI

Accession

Primary (citable) accession number: Q93K97
Secondary accession number(s): P36651, P82969, Q2M9G6

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	April 13, 2004
Last modified:	January 25, 2012
This is version 88 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program