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Protein

Probable phosphatase YcdX

Gene

ycdX

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

Functioni

Hydrolyzes p-nitrophenyl phosphate (pNPP) in vitro. Involved in the swarming motility process.1 Publication

Cofactori

Zn2+1 PublicationNote: Binds 3 Zn2+ ions per subunit.1 Publication

Enzyme regulationi

Activity is stimulated by YcdY.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Zinc 11 Publication
Metal bindingi9 – 91Zinc 11 Publication
Metal bindingi15 – 151Zinc 21 Publication
Metal bindingi40 – 401Zinc 21 Publication
Metal bindingi73 – 731Zinc 11 Publication
Metal bindingi73 – 731Zinc 31 Publication
Metal bindingi101 – 1011Zinc 31 Publication
Metal bindingi131 – 1311Zinc 31 Publication
Metal bindingi192 – 1921Zinc 11 Publication
Metal bindingi194 – 1941Zinc 21 Publication

GO - Molecular functioni

  • DNA binding Source: InterPro
  • DNA-directed DNA polymerase activity Source: InterPro
  • phosphatase activity Source: UniProtKB-HAMAP
  • phosphoric ester hydrolase activity Source: EcoCyc
  • zinc ion binding Source: EcoCyc

GO - Biological processi

  • bacterial-type flagellum-dependent swarming motility Source: EcoCyc
  • DNA replication Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G6540-MONOMER.
ECOL316407:JW1017-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable phosphatase YcdXUniRule annotation (EC:3.1.3.-UniRule annotation)
Gene namesi
Name:ycdXUniRule annotation
Ordered Locus Names:b1034, JW1017
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13870. ycdX.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Mutants show no swarming ability.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 245245Probable phosphatase YcdXPRO_0000013818Add
BLAST

Proteomic databases

PaxDbiP75914.
PRIDEiP75914.

Interactioni

Subunit structurei

Homotrimer. Interacts with YcdY.UniRule annotation2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ycdYP759152EBI-1121626,EBI-1121634

Protein-protein interaction databases

BioGridi4260061. 132 interactions.
IntActiP75914. 8 interactions.
STRINGi511145.b1034.

Structurei

Secondary structure

1
245
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi20 – 3011Combined sources
Beta strandi34 – 407Combined sources
Helixi51 – 544Combined sources
Helixi55 – 584Combined sources
Beta strandi61 – 633Combined sources
Beta strandi66 – 7611Combined sources
Helixi87 – 926Combined sources
Beta strandi94 – 996Combined sources
Turni102 – 1043Combined sources
Helixi110 – 12213Combined sources
Beta strandi127 – 1293Combined sources
Helixi141 – 15111Combined sources
Beta strandi154 – 1585Combined sources
Helixi173 – 18311Combined sources
Beta strandi187 – 1904Combined sources
Beta strandi193 – 1953Combined sources
Helixi196 – 1983Combined sources
Helixi203 – 2119Combined sources
Helixi216 – 2183Combined sources
Helixi220 – 2223Combined sources
Helixi224 – 23310Combined sources
Helixi240 – 2423Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1M65X-ray1.57A1-245[»]
1M68X-ray2.30A1-245[»]
1PB0X-ray1.95A/B/C1-245[»]
ProteinModelPortaliP75914.
SMRiP75914. Positions 2-245.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP75914.

Family & Domainsi

Sequence similaritiesi

Belongs to the PHP family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107SSZ. Bacteria.
COG1387. LUCA.
HOGENOMiHOG000218067.
InParanoidiP75914.
KOiK04477.
OMAiSEPNCRA.
PhylomeDBiP75914.

Family and domain databases

HAMAPiMF_01561. YcdX_phosphat. 1 hit.
InterProiIPR023710. Phosphatase_YcdX_put.
IPR004013. PHP_dom.
IPR003141. Pol/His_phosphatase_N.
IPR016195. Pol/histidinol_Pase-like.
[Graphical view]
PfamiPF02811. PHP. 1 hit.
[Graphical view]
SMARTiSM00481. POLIIIAc. 1 hit.
[Graphical view]
SUPFAMiSSF89550. SSF89550. 1 hit.

Sequencei

Sequence statusi: Complete.

P75914-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYPVDLHMHT VASTHAYSTL SDYIAQAKQK GIKLFAITDH GPDMEDAPHH
60 70 80 90 100
WHFINMRIWP RVVDGVGILR GIEANIKNVD GEIDCSGKMF DSLDLIIAGF
110 120 130 140 150
HEPVFAPHDK ATNTQAMIAT IASGNVHIIS HPGNPKYEID VKAVAEAAAK
160 170 180 190 200
HQVALEINNS SFLHSRKGSE DNCREVAAAV RDAGGWVALG SDSHTAFTMG
210 220 230 240
EFEECLKILD AVDFPPERIL NVSPRRLLNF LESRGMAPIA EFADL
Length:245
Mass (Da):26,891
Last modified:February 1, 1997 - v1
Checksum:i19ADC0EF462D49D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74118.1.
AP009048 Genomic DNA. Translation: BAA35815.1.
PIRiG64845.
RefSeqiNP_415552.1. NC_000913.3.
WP_000283667.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74118; AAC74118; b1034.
BAA35815; BAA35815; BAA35815.
GeneIDi948477.
KEGGiecj:JW1017.
eco:b1034.
PATRICi32117299. VBIEscCol129921_1072.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74118.1.
AP009048 Genomic DNA. Translation: BAA35815.1.
PIRiG64845.
RefSeqiNP_415552.1. NC_000913.3.
WP_000283667.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1M65X-ray1.57A1-245[»]
1M68X-ray2.30A1-245[»]
1PB0X-ray1.95A/B/C1-245[»]
ProteinModelPortaliP75914.
SMRiP75914. Positions 2-245.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260061. 132 interactions.
IntActiP75914. 8 interactions.
STRINGi511145.b1034.

Proteomic databases

PaxDbiP75914.
PRIDEiP75914.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74118; AAC74118; b1034.
BAA35815; BAA35815; BAA35815.
GeneIDi948477.
KEGGiecj:JW1017.
eco:b1034.
PATRICi32117299. VBIEscCol129921_1072.

Organism-specific databases

EchoBASEiEB3629.
EcoGeneiEG13870. ycdX.

Phylogenomic databases

eggNOGiENOG4107SSZ. Bacteria.
COG1387. LUCA.
HOGENOMiHOG000218067.
InParanoidiP75914.
KOiK04477.
OMAiSEPNCRA.
PhylomeDBiP75914.

Enzyme and pathway databases

BioCyciEcoCyc:G6540-MONOMER.
ECOL316407:JW1017-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP75914.
PROiP75914.

Family and domain databases

HAMAPiMF_01561. YcdX_phosphat. 1 hit.
InterProiIPR023710. Phosphatase_YcdX_put.
IPR004013. PHP_dom.
IPR003141. Pol/His_phosphatase_N.
IPR016195. Pol/histidinol_Pase-like.
[Graphical view]
PfamiPF02811. PHP. 1 hit.
[Graphical view]
SMARTiSM00481. POLIIIAc. 1 hit.
[Graphical view]
SUPFAMiSSF89550. SSF89550. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYCDX_ECOLI
AccessioniPrimary (citable) accession number: P75914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: September 7, 2016
This is version 126 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.