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Protein

Uncharacterized metal-dependent hydrolase YcfH

Gene

ycfH

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

Functioni

Has D-tyrosyl-tRNA deacylase activity in vitro.1 Publication

Cofactori

Co2+1 Publication, Mn2+1 Publication, Ni2+1 PublicationNote: Binds 2 divalent metal cations per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Divalent metal cation 11 Publication
Metal bindingi9 – 91Divalent metal cation 11 Publication
Metal bindingi94 – 941Divalent metal cation 11 Publication
Metal bindingi94 – 941Divalent metal cation 21 Publication
Metal bindingi130 – 1301Divalent metal cation 21 Publication
Metal bindingi155 – 1551Divalent metal cation 21 Publication
Metal bindingi205 – 2051Divalent metal cation 11 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12303-MONOMER.
ECOL316407:JW1086-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized metal-dependent hydrolase YcfHCurated (EC:3.1.-.-Curated)
Gene namesi
Name:ycfH
Ordered Locus Names:b1100, JW1086
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12303. ycfH.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 265265Uncharacterized metal-dependent hydrolase YcfHPRO_0000201995Add
BLAST

Proteomic databases

PaxDbiP0AFQ7.
PRIDEiP0AFQ7.

Interactioni

Protein-protein interaction databases

BioGridi4260943. 192 interactions.
DIPiDIP-48157N.
IntActiP0AFQ7. 8 interactions.
MINTiMINT-1267935.
STRINGi511145.b1100.

Structurei

Secondary structure

1
265
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi10 – 123Combined sources
Turni15 – 184Combined sources
Helixi22 – 3110Combined sources
Beta strandi34 – 396Combined sources
Helixi44 – 5411Combined sources
Beta strandi60 – 645Combined sources
Helixi77 – 848Combined sources
Beta strandi89 – 9810Combined sources
Helixi106 – 12318Combined sources
Beta strandi127 – 1337Combined sources
Helixi135 – 14410Combined sources
Helixi147 – 1493Combined sources
Beta strandi152 – 1543Combined sources
Helixi161 – 1688Combined sources
Turni169 – 1713Combined sources
Beta strandi173 – 1764Combined sources
Helixi178 – 1814Combined sources
Helixi186 – 1949Combined sources
Helixi197 – 1993Combined sources
Beta strandi200 – 2023Combined sources
Helixi221 – 2233Combined sources
Helixi224 – 23512Combined sources
Helixi239 – 25315Combined sources
Helixi258 – 2614Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YIXX-ray1.90A/B1-265[»]
ProteinModelPortaliP0AFQ7.
SMRiP0AFQ7. Positions 1-265.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFQ7.

Family & Domainsi

Sequence similaritiesi

Belongs to the TatD-type hydrolase family.Curated

Phylogenomic databases

eggNOGiENOG4105F8V. Bacteria.
COG0084. LUCA.
HOGENOMiHOG000201520.
InParanoidiP0AFQ7.
KOiK03424.
OMAiRAGGVFH.
OrthoDBiEOG66QM1C.
PhylomeDBiP0AFQ7.

Family and domain databases

InterProiIPR018228. DNase_TatD-rel_CS.
IPR015991. Hydrolase_TatD-type.
IPR032466. Metal_Hydrolase.
IPR001130. TatD_family.
[Graphical view]
PANTHERiPTHR10060. PTHR10060. 1 hit.
PfamiPF01026. TatD_DNase. 1 hit.
[Graphical view]
PIRSFiPIRSF005902. DNase_TatD. 1 hit.
SUPFAMiSSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR00010. TIGR00010. 1 hit.
PROSITEiPS01137. TATD_1. 1 hit.
PS01091. TATD_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AFQ7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFLVDSHCHL DGLDYESLHK DVDDVLAKAA ARDVKFCLAV ATTLPGYLHM
60 70 80 90 100
RDLVGERDNV VFSCGVHPLN QNDPYDVEDL RRLAAEEGVV ALGETGLDYY
110 120 130 140 150
YTPETKVRQQ ESFIHHIQIG RELNKPVIVH TRDARADTLA ILREEKVTDC
160 170 180 190 200
GGVLHCFTED RETAGKLLDL GFYISFSGIV TFRNAEQLRD AARYVPLDRL
210 220 230 240 250
LVETDSPYLA PVPHRGKENQ PAMVRDVAEY MAVLKGVAVE ELAQVTTDNF
260
ARLFHIDASR LQSIR
Length:265
Mass (Da):29,809
Last modified:December 20, 2005 - v1
Checksum:i722C9450157620C5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti97 – 971L → Q (PubMed:8509334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74184.1.
AP009048 Genomic DNA. Translation: BAA35907.1.
L01483 Genomic DNA. No translation available.
L04577 Genomic DNA. No translation available.
PIRiA64854.
RefSeqiNP_415618.1. NC_000913.3.
WP_000480245.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74184; AAC74184; b1100.
BAA35907; BAA35907; BAA35907.
GeneIDi945656.
KEGGiecj:JW1086.
eco:b1100.
PATRICi32117441. VBIEscCol129921_1143.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74184.1.
AP009048 Genomic DNA. Translation: BAA35907.1.
L01483 Genomic DNA. No translation available.
L04577 Genomic DNA. No translation available.
PIRiA64854.
RefSeqiNP_415618.1. NC_000913.3.
WP_000480245.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YIXX-ray1.90A/B1-265[»]
ProteinModelPortaliP0AFQ7.
SMRiP0AFQ7. Positions 1-265.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260943. 192 interactions.
DIPiDIP-48157N.
IntActiP0AFQ7. 8 interactions.
MINTiMINT-1267935.
STRINGi511145.b1100.

Proteomic databases

PaxDbiP0AFQ7.
PRIDEiP0AFQ7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74184; AAC74184; b1100.
BAA35907; BAA35907; BAA35907.
GeneIDi945656.
KEGGiecj:JW1086.
eco:b1100.
PATRICi32117441. VBIEscCol129921_1143.

Organism-specific databases

EchoBASEiEB2209.
EcoGeneiEG12303. ycfH.

Phylogenomic databases

eggNOGiENOG4105F8V. Bacteria.
COG0084. LUCA.
HOGENOMiHOG000201520.
InParanoidiP0AFQ7.
KOiK03424.
OMAiRAGGVFH.
OrthoDBiEOG66QM1C.
PhylomeDBiP0AFQ7.

Enzyme and pathway databases

BioCyciEcoCyc:EG12303-MONOMER.
ECOL316407:JW1086-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AFQ7.
PROiP0AFQ7.

Family and domain databases

InterProiIPR018228. DNase_TatD-rel_CS.
IPR015991. Hydrolase_TatD-type.
IPR032466. Metal_Hydrolase.
IPR001130. TatD_family.
[Graphical view]
PANTHERiPTHR10060. PTHR10060. 1 hit.
PfamiPF01026. TatD_DNase. 1 hit.
[Graphical view]
PIRSFiPIRSF005902. DNase_TatD. 1 hit.
SUPFAMiSSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR00010. TIGR00010. 1 hit.
PROSITEiPS01137. TATD_1. 1 hit.
PS01091. TATD_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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.
  4. "Identification, isolation, and characterization of the structural gene encoding the delta' subunit of Escherichia coli DNA polymerase III holoenzyme."
    Carter J.R., Franden M.A., Aebersold R.H., McHenry C.S.
    J. Bacteriol. 175:3812-3822(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-104.
    Strain: K12 / MG1655 / ATCC 47076.
  5. "DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'."
    Dong Z., Onrust R., Skangalis M., O'Donnell M.
    J. Biol. Chem. 268:11758-11765(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-43.
    Strain: K12.
  6. "Widespread distribution of cell defense against D-aminoacyl-tRNAs."
    Wydau S., van der Rest G., Aubard C., Plateau P., Blanquet S.
    J. Biol. Chem. 284:14096-14104(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DEACETYLASE, COFACTOR.
  7. "Crystal structure of ycfH, tatD homolog from Escherichia coli."
    New York structural genomix research consortium (NYSGXRC)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ZINC IONS.

Entry informationi

Entry nameiYCFH_ECOLI
AccessioniPrimary (citable) accession number: P0AFQ7
Secondary accession number(s): P37346, P78057
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: July 6, 2016
This is version 90 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.