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Protein

Uncharacterized Nudix hydrolase YfcD

Gene

yfcD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi88 – 881Magnesium
Metal bindingi92 – 921MagnesiumBy similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7191-MONOMER.
ECOL316407:JW2296-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized Nudix hydrolase YfcD (EC:3.6.-.-)
Gene namesi
Name:yfcD
Ordered Locus Names:b2299, JW2296
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14107. yfcD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 180180Uncharacterized Nudix hydrolase YfcDPRO_0000057077Add
BLAST

Proteomic databases

PaxDbiP65556.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
panCP316635EBI-545346,EBI-545354

Protein-protein interaction databases

BioGridi4260514. 13 interactions.
DIPiDIP-28086N.
IntActiP65556. 4 interactions.
STRINGi511145.b2299.

Structurei

Secondary structure

1
180
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63Combined sources
Beta strandi11 – 155Combined sources
Beta strandi21 – 266Combined sources
Helixi27 – 337Combined sources
Beta strandi37 – 459Combined sources
Beta strandi47 – 493Combined sources
Beta strandi51 – 566Combined sources
Beta strandi61 – 633Combined sources
Beta strandi67 – 715Combined sources
Helixi81 – 9313Combined sources
Beta strandi101 – 11010Combined sources
Beta strandi113 – 12311Combined sources
Turni132 – 1343Combined sources
Beta strandi135 – 1417Combined sources
Helixi143 – 1475Combined sources
Helixi148 – 1525Combined sources
Helixi155 – 16713Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FKBX-ray2.00A/B/C1-180[»]
ProteinModelPortaliP65556.
SMRiP65556. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP65556.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 163129Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi72 – 9423Nudix boxAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105PTV. Bacteria.
ENOG410ZCV3. LUCA.
HOGENOMiHOG000274108.
InParanoidiP65556.
OMAiGYWDVAA.
OrthoDBiEOG6CP3XQ.
PhylomeDBiP65556.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR024195. NUDIX_hydrolase_YfcD_pred.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF017340. Nudix_hydro. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P65556-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQRRLASTE WVDIVNEENE VIAQASREQM RAQCLRHRAT YIVVHDGMGK
60 70 80 90 100
ILVQRRTETK DFLPGMLDAT AGGVVQADEQ LLESARREAE EELGIAGVPF
110 120 130 140 150
AEHGQFYFED KNCRVWGALF SCVSHGPFAL QEDEVSEVCW LTPEEITARC
160 170 180
DEFTPDSLKA LALWMKRNAK NEAVETETAE
Length:180
Mass (Da):20,376
Last modified:October 11, 2004 - v1
Checksum:i83FC88B71EF9D58B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75359.1.
AP009048 Genomic DNA. Translation: BAE76686.1.
PIRiA65002.
RefSeqiNP_416802.1. NC_000913.3.
WP_000437935.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75359; AAC75359; b2299.
BAE76686; BAE76686; BAE76686.
GeneIDi946783.
KEGGiecj:JW2296.
eco:b2299.
PATRICi32119969. VBIEscCol129921_2394.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75359.1.
AP009048 Genomic DNA. Translation: BAE76686.1.
PIRiA65002.
RefSeqiNP_416802.1. NC_000913.3.
WP_000437935.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FKBX-ray2.00A/B/C1-180[»]
ProteinModelPortaliP65556.
SMRiP65556. Positions 2-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260514. 13 interactions.
DIPiDIP-28086N.
IntActiP65556. 4 interactions.
STRINGi511145.b2299.

Proteomic databases

PaxDbiP65556.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75359; AAC75359; b2299.
BAE76686; BAE76686; BAE76686.
GeneIDi946783.
KEGGiecj:JW2296.
eco:b2299.
PATRICi32119969. VBIEscCol129921_2394.

Organism-specific databases

EchoBASEiEB3860.
EcoGeneiEG14107. yfcD.

Phylogenomic databases

eggNOGiENOG4105PTV. Bacteria.
ENOG410ZCV3. LUCA.
HOGENOMiHOG000274108.
InParanoidiP65556.
OMAiGYWDVAA.
OrthoDBiEOG6CP3XQ.
PhylomeDBiP65556.

Enzyme and pathway databases

BioCyciEcoCyc:G7191-MONOMER.
ECOL316407:JW2296-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP65556.
PROiP65556.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
IPR024195. NUDIX_hydrolase_YfcD_pred.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF017340. Nudix_hydro. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 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. "Crystal structure of a putative enzyme (possible nudix hydrolase) from Escherichia coli K12."
    Midwest center for structural genomics (MCSG)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS.

Entry informationi

Entry nameiYFCD_ECOLI
AccessioniPrimary (citable) accession number: P65556
Secondary accession number(s): P76494, Q2MAM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: January 20, 2016
This is version 94 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.