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Protein

ADP-ribose pyrophosphatase

Gene

nudF

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

Functioni

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.1 Publication

Catalytic activityi

ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate.1 Publication

Cofactori

Mg2+2 PublicationsNote: Binds 3 Mg2+ ions per subunit.2 Publications

Enzyme regulationi

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei56 – 561Substrate
Binding sitei79 – 791Substrate
Metal bindingi96 – 961Magnesium 1; via carbonyl oxygen
Binding sitei98 – 981Substrate; via amide nitrogen
Metal bindingi112 – 1121Magnesium 2
Metal bindingi112 – 1121Magnesium 3
Metal bindingi116 – 1161Magnesium 1
Metal bindingi116 – 1161Magnesium 3
Binding sitei139 – 1391Substrate
Active sitei162 – 1621Proton acceptorCurated
Metal bindingi164 – 1641Magnesium 3

GO - Molecular functioni

  • ADP-ribose diphosphatase activity Source: EcoCyc
  • ADP-sugar diphosphatase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc

GO - Biological processi

  • response to heat Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12633-MONOMER.
ECOL316407:JW3002-MONOMER.
MetaCyc:EG12633-MONOMER.
BRENDAi3.6.1.13. 2026.

Names & Taxonomyi

Protein namesi
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 namesi
Name:nudF
Synonyms:aspP, yqiE, yzzG
Ordered Locus Names:b3034, JW3002
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12184. nudF.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 209209ADP-ribose pyrophosphatasePRO_0000057042Add
BLAST

Proteomic databases

PaxDbiQ93K97.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi4263247. 23 interactions.
DIPiDIP-36214N.
IntActiQ93K97. 5 interactions.
STRINGi511145.b3034.

Structurei

Secondary structure

1
209
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 103Combined sources
Helixi13 – 153Combined sources
Beta strandi16 – 3924Combined sources
Beta strandi49 – 557Combined sources
Beta strandi59 – 668Combined sources
Turni67 – 704Combined sources
Beta strandi71 – 788Combined sources
Helixi80 – 856Combined sources
Beta strandi89 – 935Combined sources
Beta strandi95 – 984Combined sources
Helixi105 – 11713Combined sources
Beta strandi124 – 1329Combined sources
Turni134 – 1363Combined sources
Beta strandi140 – 1478Combined sources
Helixi150 – 1523Combined sources
Beta strandi155 – 1573Combined sources
Turni161 – 1655Combined sources
Beta strandi167 – 1726Combined sources
Helixi173 – 1819Combined sources
Helixi188 – 20720Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G0SX-ray1.90A/B1-209[»]
1G9QX-ray2.30A/B1-209[»]
1GA7X-ray2.71A/B1-209[»]
1KHZX-ray2.04A/B1-209[»]
1VIQX-ray2.40A/B/C2-209[»]
ProteinModelPortaliQ93K97.
SMRiQ93K97. Positions 8-209.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93K97.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini55 – 193139Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni28 – 292Substrate binding
Regioni51 – 522Substrate binding; shared with dimeric partner
Regioni133 – 1353Substrate binding; shared with dimeric partner

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi97 – 11822Nudix boxAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG41087AY. Bacteria.
ENOG410ZYVG. LUCA.
HOGENOMiHOG000045857.
InParanoidiQ93K97.
KOiK01515.
OMAiEQAYQWM.
PhylomeDBiQ93K97.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR004385. NDP_pyrophosphatase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR00052. TIGR00052. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q93K97-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKPDNLPVT FGKNDVEIIA RETLYRGFFS LDLYRFRHRL FNGQMSHEVR
60 70 80 90 100
REIFERGHAA VLLPFDPVRD EVVLIEQIRI AAYDTSETPW LLEMVAGMIE
110 120 130 140 150
EGESVEDVAR REAIEEAGLI VKRTKPVLSF LASPGGTSER SSIMVGEVDA
160 170 180 190 200
TTASGIHGLA DENEDIRVHV VSREQAYQWV EEGKIDNAAS VIALQWLQLH

HQALKNEWA
Length:209
Mass (Da):23,667
Last modified:April 13, 2004 - v2
Checksum:i2CF77EA9D63B9615
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti2 – 21L → V in CAC44036 (PubMed:11416161).Curated
Sequence conflicti6 – 61N → S in CAC44036 (PubMed:11416161).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiH65090.
RefSeqiNP_417506.1. NC_000913.3.
WP_000917117.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76070; AAC76070; b3034.
BAE77090; BAE77090; BAE77090.
GeneIDi947519.
KEGGiecj:JW3002.
eco:b3034.
PATRICi32121478. VBIEscCol129921_3126.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiH65090.
RefSeqiNP_417506.1. NC_000913.3.
WP_000917117.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G0SX-ray1.90A/B1-209[»]
1G9QX-ray2.30A/B1-209[»]
1GA7X-ray2.71A/B1-209[»]
1KHZX-ray2.04A/B1-209[»]
1VIQX-ray2.40A/B/C2-209[»]
ProteinModelPortaliQ93K97.
SMRiQ93K97. Positions 8-209.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263247. 23 interactions.
DIPiDIP-36214N.
IntActiQ93K97. 5 interactions.
STRINGi511145.b3034.

Proteomic databases

PaxDbiQ93K97.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76070; AAC76070; b3034.
BAE77090; BAE77090; BAE77090.
GeneIDi947519.
KEGGiecj:JW3002.
eco:b3034.
PATRICi32121478. VBIEscCol129921_3126.

Organism-specific databases

EcoGeneiEG12184. nudF.

Phylogenomic databases

eggNOGiENOG41087AY. Bacteria.
ENOG410ZYVG. LUCA.
HOGENOMiHOG000045857.
InParanoidiQ93K97.
KOiK01515.
OMAiEQAYQWM.
PhylomeDBiQ93K97.

Enzyme and pathway databases

BioCyciEcoCyc:EG12633-MONOMER.
ECOL316407:JW3002-MONOMER.
MetaCyc:EG12633-MONOMER.
BRENDAi3.6.1.13. 2026.

Miscellaneous databases

EvolutionaryTraceiQ93K97.
PROiQ93K97.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR004385. NDP_pyrophosphatase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR00052. TIGR00052. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiADPP_ECOLI
AccessioniPrimary (citable) accession number: Q93K97
Secondary accession number(s): P36651, P82969, Q2M9G6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: April 13, 2004
Last modified: September 7, 2016
This is version 121 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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

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.