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Protein

NADH pyrophosphatase

Gene

nudC

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

Functioni

Catalyzes the hydrolysis of a broad range of dinucleotide pyrophosphates, but uniquely prefers the reduced form of NADH.1 Publication

Catalytic activityi

NAD(H) + H2O = AMP + NMN(H).1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Mg2+1 Publication, Mn2+1 PublicationNote: Divalent metal cations. Mg2+ or Mn2+.1 Publication
  • Zn2+1 PublicationNote: Binds 1 zinc ion per subunit.1 Publication

Kineticsi

  1. KM=0.11 mM for NADH1 Publication
  2. KM=5.1 mM for NAD+1 Publication
  3. KM=0.29 mM for deamino-NADH1 Publication
  4. KM=2.6 mM for deamino-NAD+1 Publication
  5. KM=0.67 mM for AppA1 Publication
  6. KM=1.8 mM for ADP-ribose1 Publication
  1. Vmax=7.6 µmol/min/mg enzyme with NADH as substrate1 Publication
  2. Vmax=2.9 µmol/min/mg enzyme with NAD+ as substrate1 Publication
  3. Vmax=8.9 µmol/min/mg enzyme with deamino-NADH as substrate1 Publication
  4. Vmax=3.2 µmol/min/mg enzyme with deamino-NAD+ as substrate1 Publication
  5. Vmax=4.7 µmol/min/mg enzyme with AppA as substrate1 Publication
  6. Vmax=4.8 µmol/min/mg enzyme with ADP-ribose as substrate1 Publication

pH dependencei

Optimum pH is 8.5.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi98Zinc1 Publication1
Metal bindingi101Zinc1 Publication1
Metal bindingi116Zinc1 Publication1
Metal bindingi119Zinc1 Publication1
Metal bindingi174Divalent metal cationBy similarity1
Metal bindingi178Divalent metal cationBy similarity1

GO - Molecular functioni

  • magnesium ion binding Source: UniProtKB-HAMAP
  • manganese ion binding Source: EcoCyc
  • NAD+ diphosphatase activity Source: UniProtKB-HAMAP
  • NADH pyrophosphatase activity Source: EcoCyc
  • zinc ion binding Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11702-MONOMER.
ECOL316407:JW5548-MONOMER.
MetaCyc:EG11702-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
NADH pyrophosphatase1 Publication (EC:3.6.1.221 Publication)
Gene namesi
Name:nudC
Synonyms:yjaD
Ordered Locus Names:b3996, JW5548
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11702. nudC.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000569631 – 257NADH pyrophosphataseAdd BLAST257

Proteomic databases

PaxDbiP32664.
PRIDEiP32664.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi4263215. 134 interactors.
IntActiP32664. 1 interactor.
STRINGi511145.b3996.

Structurei

Secondary structure

1257
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 17Combined sources8
Beta strandi20 – 22Combined sources3
Helixi24 – 26Combined sources3
Beta strandi30 – 32Combined sources3
Helixi33 – 36Combined sources4
Beta strandi42 – 58Combined sources17
Helixi70 – 74Combined sources5
Helixi76 – 93Combined sources18
Turni99 – 101Combined sources3
Beta strandi104 – 107Combined sources4
Beta strandi109 – 112Combined sources4
Beta strandi114 – 120Combined sources7
Beta strandi128 – 137Combined sources10
Beta strandi140 – 146Combined sources7
Turni147 – 149Combined sources3
Beta strandi157 – 160Combined sources4
Helixi167 – 179Combined sources13
Beta strandi182 – 194Combined sources13
Turni195 – 198Combined sources4
Beta strandi199 – 210Combined sources12
Turni217 – 219Combined sources3
Beta strandi220 – 227Combined sources8
Helixi240 – 254Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VK6X-ray2.20A1-257[»]
2GB5X-ray2.30A/B1-257[»]
5ISYX-ray2.35A/C1-257[»]
ProteinModelPortaliP32664.
SMRiP32664.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP32664.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini125 – 248Nudix hydrolasePROSITE-ProRule annotationAdd BLAST124

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi159 – 180Nudix boxPROSITE-ProRule annotationAdd BLAST22

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105E09. Bacteria.
COG2816. LUCA.
HOGENOMiHOG000247937.
InParanoidiP32664.
KOiK03426.
OMAiFERFDEW.
PhylomeDBiP32664.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00297. Nudix_NudC. 1 hit.
InterProiIPR022925. NADH_pyroPase_NudC.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR015376. Znr_NADH_PPase.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
PF09297. zf-NADH-PPase. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 2 hits.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32664-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDRIIEKLDH GWWVVSHEQK LWLPKGELPY GEAANFDLVG QRALQIGEWQ
60 70 80 90 100
GEPVWLVQQQ RRHDMGSVRQ VIDLDVGLFQ LAGRGVQLAE FYRSHKYCGY
110 120 130 140 150
CGHEMYPSKT EWAMLCSHCR ERYYPQIAPC IIVAIRRDDS ILLAQHTRHR
160 170 180 190 200
NGVHTVLAGF VEVGETLEQA VAREVMEESG IKVKNLRYVT SQPWPFPQSL
210 220 230 240 250
MTAFMAEYDS GDIVIDPKEL LEANWYRYDD LPLLPPPGTV ARRLIEDTVA

MCRAEYE
Length:257
Mass (Da):29,689
Last modified:October 11, 2004 - v2
Checksum:i368FAE0480AF4CB3
GO

Sequence cautioni

The sequence D12624 differs from that shown. Reason: Frameshift at position 116.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti33A → R in AAC43094 (PubMed:8265357).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12624 Genomic DNA. No translation available.
U00006 Genomic DNA. Translation: AAC43094.1.
U00096 Genomic DNA. Translation: AAT48238.1.
AP009048 Genomic DNA. Translation: BAE77323.1.
PIRiG65206.
RefSeqiWP_000373940.1. NZ_LN832404.1.
YP_026280.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAT48238; AAT48238; b3996.
BAE77323; BAE77323; BAE77323.
GeneIDi948498.
KEGGiecj:JW5548.
eco:b3996.
PATRICi32123515. VBIEscCol129921_4110.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D12624 Genomic DNA. No translation available.
U00006 Genomic DNA. Translation: AAC43094.1.
U00096 Genomic DNA. Translation: AAT48238.1.
AP009048 Genomic DNA. Translation: BAE77323.1.
PIRiG65206.
RefSeqiWP_000373940.1. NZ_LN832404.1.
YP_026280.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VK6X-ray2.20A1-257[»]
2GB5X-ray2.30A/B1-257[»]
5ISYX-ray2.35A/C1-257[»]
ProteinModelPortaliP32664.
SMRiP32664.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263215. 134 interactors.
IntActiP32664. 1 interactor.
STRINGi511145.b3996.

Proteomic databases

PaxDbiP32664.
PRIDEiP32664.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAT48238; AAT48238; b3996.
BAE77323; BAE77323; BAE77323.
GeneIDi948498.
KEGGiecj:JW5548.
eco:b3996.
PATRICi32123515. VBIEscCol129921_4110.

Organism-specific databases

EchoBASEiEB1653.
EcoGeneiEG11702. nudC.

Phylogenomic databases

eggNOGiENOG4105E09. Bacteria.
COG2816. LUCA.
HOGENOMiHOG000247937.
InParanoidiP32664.
KOiK03426.
OMAiFERFDEW.
PhylomeDBiP32664.

Enzyme and pathway databases

BioCyciEcoCyc:EG11702-MONOMER.
ECOL316407:JW5548-MONOMER.
MetaCyc:EG11702-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP32664.
PROiP32664.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00297. Nudix_NudC. 1 hit.
InterProiIPR022925. NADH_pyroPase_NudC.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR015376. Znr_NADH_PPase.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
PF09297. zf-NADH-PPase. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 2 hits.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNUDC_ECOLI
AccessioniPrimary (citable) accession number: P32664
Secondary accession number(s): Q2M8T3, Q6BEX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 11, 2004
Last modified: November 2, 2016
This is version 135 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, 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.