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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)DescriptionActionsGraphical viewLength
Binding sitei56Substrate1
Binding sitei79Substrate1
Metal bindingi96Magnesium 1; via carbonyl oxygen1
Binding sitei98Substrate; via amide nitrogen1
Metal bindingi112Magnesium 21
Metal bindingi112Magnesium 31
Metal bindingi116Magnesium 11
Metal bindingi116Magnesium 31
Binding sitei139Substrate1
Active sitei162Proton acceptorCurated1
Metal bindingi164Magnesium 31

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00000570421 – 209ADP-ribose pyrophosphataseAdd BLAST209

Proteomic databases

PaxDbiQ93K97.
PRIDEiQ93K97.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1209
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 10Combined sources3
Helixi13 – 15Combined sources3
Beta strandi16 – 39Combined sources24
Beta strandi49 – 55Combined sources7
Beta strandi59 – 66Combined sources8
Turni67 – 70Combined sources4
Beta strandi71 – 78Combined sources8
Helixi80 – 85Combined sources6
Beta strandi89 – 93Combined sources5
Beta strandi95 – 98Combined sources4
Helixi105 – 117Combined sources13
Beta strandi124 – 132Combined sources9
Turni134 – 136Combined sources3
Beta strandi140 – 147Combined sources8
Helixi150 – 152Combined sources3
Beta strandi155 – 157Combined sources3
Turni161 – 165Combined sources5
Beta strandi167 – 172Combined sources6
Helixi173 – 181Combined sources9
Helixi188 – 207Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93K97.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini55 – 193Nudix hydrolasePROSITE-ProRule annotationAdd BLAST139

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni28 – 29Substrate binding2
Regioni51 – 52Substrate binding; shared with dimeric partner2
Regioni133 – 135Substrate binding; shared with dimeric partner3

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi97 – 118Nudix boxAdd BLAST22

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)DescriptionActionsGraphical viewLength
Sequence conflicti2L → V in CAC44036 (PubMed:11416161).Curated1
Sequence conflicti6N → S in CAC44036 (PubMed:11416161).Curated1

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiQ93K97.
PRIDEiQ93K97.

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: 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

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.