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Protein

PKHD-type hydroxylase YbiX

Gene

ybiX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Cofactori

Protein has several cofactor binding sites:
  • Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity
  • L-ascorbateBy similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi96IronBy similarity1
Metal bindingi98IronBy similarity1
Metal bindingi158IronBy similarity1
Binding sitei1682-oxoglutarateSequence analysis1

GO - Molecular functioni

GO - Biological processi

  • cellular iron ion homeostasis Source: EcoCyc
  • cellular response to DNA damage stimulus Source: EcoliWiki

Keywordsi

Molecular functionDioxygenase, Oxidoreductase
LigandIron, Metal-binding, Vitamin C

Enzyme and pathway databases

BioCyciEcoCyc:G6413-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PKHD-type hydroxylase YbiX (EC:1.14.11.-)
Gene namesi
Name:ybiX
Ordered Locus Names:b0804, JW5105
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13316. ybiX.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002066761 – 225PKHD-type hydroxylase YbiXAdd BLAST225

Proteomic databases

PaxDbiP75779.
PRIDEiP75779.

Interactioni

Protein-protein interaction databases

BioGridi4259955. 2 interactors.
STRINGi511145.b0804.

Structurei

3D structure databases

ProteinModelPortaliP75779.
SMRiP75779.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini78 – 177Fe2OG dioxygenaseAdd BLAST100

Phylogenomic databases

eggNOGiENOG4107E2E. Bacteria.
COG3128. LUCA.
HOGENOMiHOG000236239.
InParanoidiP75779.
KOiK07336.
OMAiDMVLYPG.
PhylomeDBiP75779.

Family and domain databases

HAMAPiMF_00657. Hydroxyl_YbiX. 1 hit.
InterProiView protein in InterPro
IPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR023550. PKHD_hydroxylase.
IPR006620. Pro_4_hyd_alph.
PfamiView protein in Pfam
PF13640. 2OG-FeII_Oxy_3. 1 hit.
SMARTiView protein in SMART
SM00702. P4Hc. 1 hit.
PROSITEiView protein in PROSITE
PS51471. FE2OG_OXY. 1 hit.

Sequencei

Sequence statusi: Complete.

P75779-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMYHIPGVLS PQDVARFREQ LEQAEWVDGR VTTGAQGAQV KNNQQVDTRS
60 70 80 90 100
TLYAALQNEV LNAVNQHALF FAAALPRTLS TPLFNRYQNN ETYGFHVDGA
110 120 130 140 150
VRSHPQNGWM RTDLSATLFL SDPQSYDGGE LVVNDTFGQH RVKLPAGDLV
160 170 180 190 200
LYPSSSLHCV TPVTRGVRVA SFMWIQSMIR DDKKRAMLFE LDNNIQSLKS
210 220
RYGESEEILS LLNLYHNLLR EWSEI
Length:225
Mass (Da):25,529
Last modified:April 27, 2001 - v2
Checksum:i001CB789CC498421
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73891.2.
AP009048 Genomic DNA. Translation: BAA35470.2.
PIRiD64817.
RefSeqiNP_415325.4. NC_000913.3.
WP_000990177.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73891; AAC73891; b0804.
BAA35470; BAA35470; BAA35470.
GeneIDi947502.
KEGGiecj:JW5105.
eco:b0804.
PATRICi32116811. VBIEscCol129921_0831.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73891.2.
AP009048 Genomic DNA. Translation: BAA35470.2.
PIRiD64817.
RefSeqiNP_415325.4. NC_000913.3.
WP_000990177.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP75779.
SMRiP75779.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259955. 2 interactors.
STRINGi511145.b0804.

Proteomic databases

PaxDbiP75779.
PRIDEiP75779.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73891; AAC73891; b0804.
BAA35470; BAA35470; BAA35470.
GeneIDi947502.
KEGGiecj:JW5105.
eco:b0804.
PATRICi32116811. VBIEscCol129921_0831.

Organism-specific databases

EchoBASEiEB3100.
EcoGeneiEG13316. ybiX.

Phylogenomic databases

eggNOGiENOG4107E2E. Bacteria.
COG3128. LUCA.
HOGENOMiHOG000236239.
InParanoidiP75779.
KOiK07336.
OMAiDMVLYPG.
PhylomeDBiP75779.

Enzyme and pathway databases

BioCyciEcoCyc:G6413-MONOMER.

Miscellaneous databases

PROiPR:P75779.

Family and domain databases

HAMAPiMF_00657. Hydroxyl_YbiX. 1 hit.
InterProiView protein in InterPro
IPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR023550. PKHD_hydroxylase.
IPR006620. Pro_4_hyd_alph.
PfamiView protein in Pfam
PF13640. 2OG-FeII_Oxy_3. 1 hit.
SMARTiView protein in SMART
SM00702. P4Hc. 1 hit.
PROSITEiView protein in PROSITE
PS51471. FE2OG_OXY. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYBIX_ECOLI
AccessioniPrimary (citable) accession number: P75779
Secondary accession number(s): Q9R7S1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: April 27, 2001
Last modified: February 15, 2017
This is version 122 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene

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.