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Protein

ADP compounds hydrolase NudE

Gene

nudE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Active on adenosine(5')triphospho(5')adenosine (Ap3A), ADP-ribose, NADH, adenosine(5')diphospho(5')adenosine (Ap2A).

Catalytic activityi

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

Cofactori

Mg2+Note: Mg2+. Other divalent cations can also be used.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei40 – 401Substrate; via amide nitrogen and carbonyl oxygen1 Publication
Metal bindingi95 – 951Divalent metal cationBy similarity
Metal bindingi99 – 991Divalent metal cationBy similarity
Binding sitei118 – 1181Substrate; via carbonyl oxygen1 Publication

GO - Molecular functioni

  • ADP-sugar diphosphatase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7740-MONOMER.
ECOL316407:JW3360-MONOMER.
MetaCyc:G7740-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ADP compounds hydrolase NudE (EC:3.6.1.-)
Gene namesi
Name:nudE
Synonyms:yrfE
Ordered Locus Names:b3397, JW3360
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12926. nudE.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 186186ADP compounds hydrolase NudEPRO_0000056989Add
BLAST

Proteomic databases

EPDiP45799.
PaxDbiP45799.
PRIDEiP45799.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4261276. 223 interactions.
IntActiP45799. 1 interaction.
STRINGi511145.b3397.

Structurei

Secondary structure

1
186
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 1810Combined sources
Beta strandi23 – 308Combined sources
Beta strandi36 – 427Combined sources
Beta strandi49 – 568Combined sources
Beta strandi59 – 679Combined sources
Turni68 – 714Combined sources
Beta strandi72 – 765Combined sources
Beta strandi78 – 814Combined sources
Helixi88 – 10013Combined sources
Beta strandi101 – 11414Combined sources
Turni117 – 1193Combined sources
Beta strandi123 – 13412Combined sources
Beta strandi147 – 1515Combined sources
Helixi152 – 1609Combined sources
Turni162 – 1643Combined sources
Helixi167 – 18216Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VHGX-ray2.70A/B2-186[»]
1VHZX-ray2.32A/B2-186[»]
ProteinModelPortaliP45799.
SMRiP45799. Positions 2-186.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45799.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini45 – 172128Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi80 – 10122Nudix boxAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4107RK2. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000045856.
InParanoidiP45799.
KOiK08312.
OMAiGTHSYEL.
OrthoDBiEOG6ZH2H1.
PhylomeDBiP45799.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P45799-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKSLQKPTI LNVETVARSR LFTVESVDLE FSNGVRRVYE RMRPTNREAV
60 70 80 90 100
MIVPIVDDHL ILIREYAVGT ESYELGFSKG LIDPGESVYE AANRELKEEV
110 120 130 140 150
GFGANDLTFL KKLSMAPSYF SSKMNIVVAQ DLYPESLEGD EPEPLPQVRW
160 170 180
PLAHMMDLLE DPDFNEARNV SALFLVREWL KGQGRV
Length:186
Mass (Da):21,153
Last modified:November 1, 1995 - v1
Checksum:iD959AD8ECF73FCC4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA58194.1.
U00096 Genomic DNA. Translation: AAC76422.1.
AP009048 Genomic DNA. Translation: BAE77894.1.
PIRiH65134.
RefSeqiNP_417856.1. NC_000913.3.
WP_000045744.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76422; AAC76422; b3397.
BAE77894; BAE77894; BAE77894.
GeneIDi947906.
KEGGiecj:JW3360.
eco:b3397.
PATRICi32122226. VBIEscCol129921_3490.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA58194.1.
U00096 Genomic DNA. Translation: AAC76422.1.
AP009048 Genomic DNA. Translation: BAE77894.1.
PIRiH65134.
RefSeqiNP_417856.1. NC_000913.3.
WP_000045744.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VHGX-ray2.70A/B2-186[»]
1VHZX-ray2.32A/B2-186[»]
ProteinModelPortaliP45799.
SMRiP45799. Positions 2-186.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261276. 223 interactions.
IntActiP45799. 1 interaction.
STRINGi511145.b3397.

Proteomic databases

EPDiP45799.
PaxDbiP45799.
PRIDEiP45799.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76422; AAC76422; b3397.
BAE77894; BAE77894; BAE77894.
GeneIDi947906.
KEGGiecj:JW3360.
eco:b3397.
PATRICi32122226. VBIEscCol129921_3490.

Organism-specific databases

EchoBASEiEB2762.
EcoGeneiEG12926. nudE.

Phylogenomic databases

eggNOGiENOG4107RK2. Bacteria.
COG0494. LUCA.
HOGENOMiHOG000045856.
InParanoidiP45799.
KOiK08312.
OMAiGTHSYEL.
OrthoDBiEOG6ZH2H1.
PhylomeDBiP45799.

Enzyme and pathway databases

BioCyciEcoCyc:G7740-MONOMER.
ECOL316407:JW3360-MONOMER.
MetaCyc:G7740-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP45799.
PROiP45799.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Orf186 represents a new member of the Nudix hydrolases, active on adenosine(5')triphospho(5')adenosine, ADP-ribose, and NADH."
    O'Handley S.F., Frick D.N., Dunn C.A., Bessman M.J.
    J. Biol. Chem. 273:3192-3197(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  4. Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 2-186 IN COMPLEX WITH SUBSTRATE, SUBUNIT.

Entry informationi

Entry nameiNUDE_ECOLI
AccessioniPrimary (citable) accession number: P45799
Secondary accession number(s): Q2M762
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: April 13, 2016
This is version 124 of the entry and version 1 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.