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Protein

Phosphodiesterase YfcE

Gene

yfcE

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

Functioni

Shows phosphodiesterase activity, hydrolyzing phosphodiesters bonds in the artificial chromogenic substrates bis-p-nitrophenyl phosphate (bis-pNPP), and less efficiently thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP) and p-nitrophenylphosphorylcholine (pNPPC). The physiological substrate is unknown.1 Publication

Cofactori

Mn2+1 PublicationNote: Binds 2 manganese ions per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Manganese 1
Metal bindingi11 – 111Manganese 1
Metal bindingi37 – 371Manganese 1
Metal bindingi37 – 371Manganese 2
Metal bindingi73 – 731Manganese 2
Metal bindingi105 – 1051Manganese 2
Metal bindingi127 – 1271Manganese 2
Metal bindingi129 – 1291Manganese 1

GO - Molecular functioni

  • hydrolase activity Source: UniProtKB-KW
  • zinc ion binding Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7192-MONOMER.
ECOL316407:JW5377-MONOMER.
BRENDAi3.1.4.1. 2026.
3.1.4.16. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphodiesterase YfcE (EC:3.1.4.-)
Gene namesi
Name:yfcE
Ordered Locus Names:b2300, JW5377
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14108. yfcE.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184Phosphodiesterase YfcEPRO_0000155605Add
BLAST

Proteomic databases

PaxDbiP67095.
PRIDEiP67095.

Interactioni

Protein-protein interaction databases

BioGridi4260515. 360 interactions.
STRINGi511145.b2300.

Structurei

Secondary structure

1
184
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Helixi14 – 2714Combined sources
Beta strandi30 – 345Combined sources
Helixi53 – 619Combined sources
Helixi62 – 665Combined sources
Beta strandi67 – 693Combined sources
Helixi77 – 826Combined sources
Beta strandi83 – 853Combined sources
Beta strandi90 – 956Combined sources
Beta strandi100 – 1045Combined sources
Beta strandi106 – 1105Combined sources
Beta strandi122 – 1243Combined sources
Beta strandi132 – 1365Combined sources
Beta strandi139 – 1435Combined sources
Beta strandi157 – 1626Combined sources
Beta strandi165 – 1706Combined sources
Turni171 – 1733Combined sources
Beta strandi176 – 1816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SU1X-ray2.25A/B/C/D1-184[»]
ProteinModelPortaliP67095.
SMRiP67095. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67095.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108RE9. Bacteria.
COG0622. LUCA.
HOGENOMiHOG000293432.
InParanoidiP67095.
KOiK07095.
OMAiDILYHGP.
OrthoDBiEOG6W45XC.
PhylomeDBiP67095.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR020935. PdiEstase_YfcE_CS.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view]
PANTHERiPTHR11124. PTHR11124. 1 hit.
PfamiPF12850. Metallophos_2. 1 hit.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR00040. yfcE. 1 hit.
PROSITEiPS01269. UPF0025. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P67095-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMKLMFASDI HGSLPATERV LELFAQSGAQ WLVILGDVLN HGPRNALPEG
60 70 80 90 100
YAPAKVAERL NEVAHKVIAV RGNCDSEVDQ MLLHFPITAP WQQVLLEKQR
110 120 130 140 150
LFLTHGHLFG PENLPALNQN DVLVYGHTHL PVAEQRGEIF HFNPGSVSIP
160 170 180
KGGNPASYGM LDNDVLSVIA LNDQSIIAQV AINP
Length:184
Mass (Da):20,122
Last modified:October 11, 2004 - v1
Checksum:i15C5AA0BE6541AB6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75360.1.
AP009048 Genomic DNA. Translation: BAE76687.1.
PIRiB65002.
RefSeqiNP_416803.3. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC75360; AAC75360; b2300.
BAE76687; BAE76687; BAE76687.
GeneIDi946755.
KEGGiecj:JW5377.
eco:b2300.
PATRICi32119971. VBIEscCol129921_2395.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75360.1.
AP009048 Genomic DNA. Translation: BAE76687.1.
PIRiB65002.
RefSeqiNP_416803.3. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SU1X-ray2.25A/B/C/D1-184[»]
ProteinModelPortaliP67095.
SMRiP67095. Positions 1-184.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260515. 360 interactions.
STRINGi511145.b2300.

Proteomic databases

PaxDbiP67095.
PRIDEiP67095.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75360; AAC75360; b2300.
BAE76687; BAE76687; BAE76687.
GeneIDi946755.
KEGGiecj:JW5377.
eco:b2300.
PATRICi32119971. VBIEscCol129921_2395.

Organism-specific databases

EchoBASEiEB3861.
EcoGeneiEG14108. yfcE.

Phylogenomic databases

eggNOGiENOG4108RE9. Bacteria.
COG0622. LUCA.
HOGENOMiHOG000293432.
InParanoidiP67095.
KOiK07095.
OMAiDILYHGP.
OrthoDBiEOG6W45XC.
PhylomeDBiP67095.

Enzyme and pathway databases

BioCyciEcoCyc:G7192-MONOMER.
ECOL316407:JW5377-MONOMER.
BRENDAi3.1.4.1. 2026.
3.1.4.16. 2026.

Miscellaneous databases

EvolutionaryTraceiP67095.
PROiP67095.

Family and domain databases

Gene3Di3.60.21.10. 1 hit.
InterProiIPR024654. Calcineurin-like_PHP_lpxH.
IPR029052. Metallo-depent_PP-like.
IPR020935. PdiEstase_YfcE_CS.
IPR000979. Phosphodiesterase_MJ0936/Vps29.
[Graphical view]
PANTHERiPTHR11124. PTHR11124. 1 hit.
PfamiPF12850. Metallophos_2. 1 hit.
[Graphical view]
SUPFAMiSSF56300. SSF56300. 1 hit.
TIGRFAMsiTIGR00040. yfcE. 1 hit.
PROSITEiPS01269. UPF0025. 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. "Enzyme genomics: application of general enzymatic screens to discover new enzymes."
    Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A., Arrowsmith C.H., Edwards A.M., Yakunin A.F.
    FEMS Microbiol. Rev. 29:263-279(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR.
  4. "Structural and biochemical characterization of YfcE, a phosphoesterase from E. coli."
    Miller D.J., Shuvalova L., Evdokimova E., Savchenko A., Yakunin A.F., Anderson W.F.
    Submitted (AUG-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).

Entry informationi

Entry nameiYFCE_ECOLI
AccessioniPrimary (citable) accession number: P67095
Secondary accession number(s): P76495, Q2MAL9
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
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.