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Protein

ADP-sugar pyrophosphatase

Gene

NUDT5

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Enzyme that can either act as an ADP-sugar pyrophosphatase in absence of diphosphate or catalyze the synthesis of ATP in presence of diphosphate (PubMed:27257257). In absence of diphosphate, hydrolyzes with similar activities various modified nucleoside diphosphates such as ADP-ribose, ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP (PubMed:10567213, PubMed:10722730, PubMed:19699693, PubMed:21389046, PubMed:17052728). Can also hydrolyze other nucleotide sugars with low activity (PubMed:19699693, PubMed:21389046). In presence of diphosphate, mediates the synthesis of ATP in the nucleus by catalyzing the conversion of ADP-ribose to ATP and ribose 5-phosphate. Nuclear ATP synthesis takes place when dephosphorylated at Thr-45 (PubMed:27257257). Nuclear ATP generation is required for extensive chromatin remodeling events that are energy-consuming (PubMed:27257257). Does not play a role in U8 snoRNA decapping activity (By similarity). Binds U8 snoRNA (By similarity).By similarity6 Publications

Catalytic activityi

ATP + D-ribose 5-phosphate = diphosphate + ADP-D-ribose.1 Publication
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate.2 Publications
ADP-sugar + H2O = AMP + alpha-D-aldose 5-phosphate.2 Publications
8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.3 Publications

Cofactori

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

Kineticsi

kcat is 0.369 min(-1) for 8-OH-dGDP. kcat is 0.538 min(-1) for 8-OH-dADP. kcat is 0.226 min(-1) for 2-OH-dADP. kcat is 0.209 min(-1) for 5-CHO-dUDP. kcat is 0.929 min(-1) for dGDP. kcat is 0.365 min(-1) for dADP.1 Publication

  1. KM=2.1 µM for 8-oxo-dGDP1 Publication
  2. KM=2.9 µM for 8-oxo-dADP1 Publication
  3. KM=8.8 µM for 2-oxo-dADP1 Publication
  4. KM=4.0 µM for 5-CHO-dUDP1 Publication
  5. KM=7.6 µM for dGDP1 Publication
  6. KM=12.6 µM for dADP1 Publication
  7. KM=3.8 µM for 8-oxo-dGDP (at pH 8.0)1 Publication
  8. KM=3.5 µM for 8-oxo-dGDP (at pH 10.0)1 Publication
  9. KM=1.9 µM for ADP-D-ribose (at pH 8.0)1 Publication
  10. KM=36 µM for 8-oxo-dGTP (at pH 10.0)1 Publication
  11. KM=42.6 µM for ADP-D-ribose (in the presence of diphosphate)1 Publication
  1. Vmax=11 pmol/min/µg enzyme with 8-oxo-dGDP as substrate (at pH 8.0)1 Publication
  2. Vmax=2400 pmol/min/µg enzyme with ADP-D-ribose as substrate (at pH 8.0)1 Publication
  3. Vmax=46 pmol/min/µg enzyme with 8-oxo-dGDP as substrate (at pH 10.0)1 Publication
  4. Vmax=1.7 pmol/min/µg enzyme with 8-oxo-dGTP as substrate (at pH 10.0)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei28 – 281Substrate3 Publications
Binding sitei51 – 511Substrate; shared with dimeric partner3 Publications
Binding sitei84 – 841Substrate3 Publications
Metal bindingi96 – 961Magnesium 1; via carbonyl oxygen3 Publications
Binding sitei98 – 981Substrate; via amide nitrogen1 Publication
Metal bindingi112 – 1121Magnesium 23 Publications
Metal bindingi112 – 1121Magnesium 33 Publications
Metal bindingi116 – 1161Magnesium 13 Publications
Metal bindingi116 – 1161Magnesium 33 Publications
Binding sitei133 – 1331Substrate1 Publication
Metal bindingi166 – 1661Magnesium 33 Publications

GO - Molecular functioni

  • ADP-ribose diphosphatase activity Source: Reactome
  • ADP-sugar diphosphatase activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • nucleoside-diphosphatase activity Source: Ensembl
  • snoRNA binding Source: UniProtKB

GO - Biological processi

  • D-ribose catabolic process Source: UniProtKB
  • nucleobase-containing small molecule catabolic process Source: Reactome
  • nucleotide metabolic process Source: ProtInc
  • ribonucleoside diphosphate catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Transferase

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

BRENDAi3.6.1.13. 2681.
3.6.1.58. 2681.
ReactomeiR-HSA-2393930. Phosphate bond hydrolysis by NUDT proteins.
SABIO-RKQ9UKK9.

Names & Taxonomyi

Protein namesi
Recommended name:
ADP-sugar pyrophosphatase (EC:3.6.1.132 Publications)
Alternative name(s):
8-oxo-dGDP phosphatase (EC:3.6.1.583 Publications)
Nuclear ATP-synthesis protein NUDIX51 Publication (EC:2.7.7.-1 Publication)
Nucleoside diphosphate-linked moiety X motif 5Curated
Short name:
Nudix motif 5Curated
Short name:
hNUDT51 Publication
YSA1H1 Publication
Gene namesi
Name:NUDT5
Synonyms:NUDIX51 Publication
ORF Names:HSPC1151 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:8052. NUDT5.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • extracellular exosome Source: UniProtKB
  • intracellular Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi28 – 281W → A: Reduces affinity for substrate about 8-fold. Strongly reduced catalytic activity and strongly reduced affinity for substrate; when associated with A-46. 1 Publication
Mutagenesisi45 – 451T → A: Impaired phosphorylation; generates ATP in the presence of diphosphate. 1 Publication
Mutagenesisi45 – 451T → D: Phosphomimetic mutant; unable to generate ATP in the presence of diphosphate. 1 Publication
Mutagenesisi46 – 461W → A: Reduces affinity for substrate about 6-fold. Strongly reduced catalytic activity and strongly reduced affinity for substrate; when associated with A-28. 1 Publication
Mutagenesisi51 – 511R → Q: Reduces affinity for substrate about 15-fold and reduces catalytic rate about 17-fold. 1 Publication
Mutagenesisi84 – 841R → Q: Reduces affinity for substrate about 5-fold and reduces catalytic rate 67-fold. 1 Publication
Mutagenesisi98 – 981L → A: Reduces affinity for substrate about 6-fold. 1 Publication
Mutagenesisi112 – 1121E → Q: Catalytic inactive mutant for both ADP-sugar pyrophosphatase and nuclear ATP-synthesis activities. Reduces catalytic rate 6300-fold. 2 Publications
Mutagenesisi116 – 1161E → Q: Reduces catalytic rate 2000-fold. 1 Publication
Mutagenesisi166 – 1661E → Q: Reduces catalytic rate 120-fold. 1 Publication

Organism-specific databases

PharmGKBiPA31838.

Polymorphism and mutation databases

BioMutaiNUDT5.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 219219ADP-sugar pyrophosphatasePRO_0000057048Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineCombined sources
Modified residuei3 – 31PhosphoserineCombined sources
Modified residuei10 – 101PhosphoserineCombined sources
Modified residuei45 – 451Phosphothreonine1 Publication
Modified residuei74 – 741PhosphotyrosineCombined sources
Modified residuei210 – 2101N6-acetyllysineCombined sources
Modified residuei218 – 2181N6-acetyllysineCombined sources

Post-translational modificationi

Phosphorylation at Thr-45 is required for homodimer stability; dephosphorylation results in destabilization of the homodimer. Dephosphorylation at Thr-45 promotes the ATP-synthesis activity.1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9UKK9.
MaxQBiQ9UKK9.
PaxDbiQ9UKK9.
PeptideAtlasiQ9UKK9.
PRIDEiQ9UKK9.

PTM databases

iPTMnetiQ9UKK9.
PhosphoSiteiQ9UKK9.

Expressioni

Tissue specificityi

Widely expressed. Most abundant in liver.1 Publication

Inductioni

Overexpressed in cancer patients with a poor outcome.1 Publication

Gene expression databases

BgeeiENSG00000165609.
CleanExiHS_NUDT5.
ExpressionAtlasiQ9UKK9. baseline and differential.
GenevisibleiQ9UKK9. HS.

Organism-specific databases

HPAiHPA019827.

Interactioni

Subunit structurei

Homodimer (PubMed:27257257, PubMed:17052728, PubMed:18462755, PubMed:21768126). Interacts with PARG (PubMed:27257257).4 Publications

Protein-protein interaction databases

BioGridi116335. 18 interactions.
IntActiQ9UKK9. 9 interactions.
MINTiMINT-1370495.
STRINGi9606.ENSP00000419628.

Structurei

Secondary structure

1
219
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 2510Combined sources
Beta strandi27 – 3711Combined sources
Beta strandi43 – 519Combined sources
Beta strandi60 – 6910Combined sources
Beta strandi76 – 849Combined sources
Helixi85 – 873Combined sources
Beta strandi89 – 935Combined sources
Beta strandi96 – 983Combined sources
Helixi105 – 11713Combined sources
Beta strandi122 – 1265Combined sources
Beta strandi130 – 1323Combined sources
Turni134 – 1363Combined sources
Beta strandi140 – 14910Combined sources
Helixi153 – 1553Combined sources
Beta strandi164 – 1663Combined sources
Beta strandi169 – 1746Combined sources
Helixi175 – 1773Combined sources
Helixi178 – 18912Combined sources
Beta strandi192 – 1943Combined sources
Helixi195 – 20713Combined sources
Turni211 – 2133Combined sources
Helixi214 – 2163Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DSBX-ray2.50A/B/C/D1-219[»]
2DSCX-ray2.00A/B1-210[»]
2DSDX-ray2.60A/B1-210[»]
3AC9X-ray2.10A/B14-208[»]
3ACAX-ray2.05A/B13-208[»]
3BM4X-ray2.00A/B1-210[»]
3L85X-ray2.30A/B14-208[»]
ProteinModelPortaliQ9UKK9.
SMRiQ9UKK9. Positions 13-209.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UKK9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini57 – 197141Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 472Substrate binding; shared with dimeric partner3 Publications

Motif

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

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG3041. Eukaryota.
COG0494. LUCA.
GeneTreeiENSGT00390000006280.
HOGENOMiHOG000174302.
HOVERGENiHBG052691.
InParanoidiQ9UKK9.
KOiK13987.
PhylomeDBiQ9UKK9.
TreeFamiTF106347.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020476. Nudix_hydrolase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR00502. NUDIXFAMILY.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9UKK9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MESQEPTESS QNGKQYIISE ELISEGKWVK LEKTTYMDPT GKTRTWESVK
60 70 80 90 100
RTTRKEQTAD GVAVIPVLQR TLHYECIVLV KQFRPPMGGY CIEFPAGLID
110 120 130 140 150
DGETPEAAAL RELEEETGYK GDIAECSPAV CMDPGLSNCT IHIVTVTING
160 170 180 190 200
DDAENARPKP KPGDGEFVEV ISLPKNDLLQ RLDALVAEEH LTVDARVYSY
210
ALALKHANAK PFEVPFLKF
Length:219
Mass (Da):24,328
Last modified:May 1, 2000 - v1
Checksum:i6574E0BF1EA2BB26
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti50 – 523KRT → NVP in AAF25479 (PubMed:10722730).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti123 – 1231I → T.
Corresponds to variant rs34863826 [ dbSNP | Ensembl ].
VAR_034159

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF155832 mRNA. Translation: AAF06734.1.
AF218818 mRNA. Translation: AAF25479.1.
AF161464 mRNA. Translation: AAF29079.1.
CR457195 mRNA. Translation: CAG33476.1.
AK291131 mRNA. Translation: BAF83820.1.
CH471072 Genomic DNA. Translation: EAW86322.1.
BC000025 mRNA. Translation: AAH00025.1.
CCDSiCCDS7089.1.
RefSeqiNP_054861.2. NM_014142.3.
UniGeneiHs.555956.
Hs.656304.

Genome annotation databases

EnsembliENST00000491614; ENSP00000419628; ENSG00000165609.
ENST00000537776; ENSP00000445116; ENSG00000165609.
GeneIDi11164.
KEGGihsa:11164.
UCSCiuc001ilj.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF155832 mRNA. Translation: AAF06734.1.
AF218818 mRNA. Translation: AAF25479.1.
AF161464 mRNA. Translation: AAF29079.1.
CR457195 mRNA. Translation: CAG33476.1.
AK291131 mRNA. Translation: BAF83820.1.
CH471072 Genomic DNA. Translation: EAW86322.1.
BC000025 mRNA. Translation: AAH00025.1.
CCDSiCCDS7089.1.
RefSeqiNP_054861.2. NM_014142.3.
UniGeneiHs.555956.
Hs.656304.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DSBX-ray2.50A/B/C/D1-219[»]
2DSCX-ray2.00A/B1-210[»]
2DSDX-ray2.60A/B1-210[»]
3AC9X-ray2.10A/B14-208[»]
3ACAX-ray2.05A/B13-208[»]
3BM4X-ray2.00A/B1-210[»]
3L85X-ray2.30A/B14-208[»]
ProteinModelPortaliQ9UKK9.
SMRiQ9UKK9. Positions 13-209.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116335. 18 interactions.
IntActiQ9UKK9. 9 interactions.
MINTiMINT-1370495.
STRINGi9606.ENSP00000419628.

PTM databases

iPTMnetiQ9UKK9.
PhosphoSiteiQ9UKK9.

Polymorphism and mutation databases

BioMutaiNUDT5.

Proteomic databases

EPDiQ9UKK9.
MaxQBiQ9UKK9.
PaxDbiQ9UKK9.
PeptideAtlasiQ9UKK9.
PRIDEiQ9UKK9.

Protocols and materials databases

DNASUi11164.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000491614; ENSP00000419628; ENSG00000165609.
ENST00000537776; ENSP00000445116; ENSG00000165609.
GeneIDi11164.
KEGGihsa:11164.
UCSCiuc001ilj.4. human.

Organism-specific databases

CTDi11164.
GeneCardsiNUDT5.
HGNCiHGNC:8052. NUDT5.
HPAiHPA019827.
MIMi609230. gene.
neXtProtiNX_Q9UKK9.
PharmGKBiPA31838.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3041. Eukaryota.
COG0494. LUCA.
GeneTreeiENSGT00390000006280.
HOGENOMiHOG000174302.
HOVERGENiHBG052691.
InParanoidiQ9UKK9.
KOiK13987.
PhylomeDBiQ9UKK9.
TreeFamiTF106347.

Enzyme and pathway databases

BRENDAi3.6.1.13. 2681.
3.6.1.58. 2681.
ReactomeiR-HSA-2393930. Phosphate bond hydrolysis by NUDT proteins.
SABIO-RKQ9UKK9.

Miscellaneous databases

ChiTaRSiNUDT5. human.
EvolutionaryTraceiQ9UKK9.
GeneWikiiNUDT5.
GenomeRNAii11164.
PROiQ9UKK9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165609.
CleanExiHS_NUDT5.
ExpressionAtlasiQ9UKK9. baseline and differential.
GenevisibleiQ9UKK9. HS.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020476. Nudix_hydrolase.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PRINTSiPR00502. NUDIXFAMILY.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNUDT5_HUMAN
AccessioniPrimary (citable) accession number: Q9UKK9
Secondary accession number(s): A8K516, Q6IAG0, Q9UH49
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: May 1, 2000
Last modified: September 7, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.