pdxY:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

PdxY

Synonyms

pyridoxal kinase 2/pyridoxine kinase[1], B1636[2][1], YdgS[2][1], PdxY[2][1] , ECK1632, JW1628, ydgS, b1636

Product description

pyridoxal kinase 2[2][3]

Pyridoxal kinase[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004340

glucokinase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01639

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01639

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01639

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01639

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008478

pyridoxal kinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004625

F

Seeded from EcoCyc (v14.0)

complete

GO:0008478

pyridoxal kinase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.1.35

F

Seeded from EcoCyc (v14.0)

complete

GO:0009443

pyridoxal 5'-phosphate salvage

PMID:9537380[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0008478

pyridoxal kinase activity

PMID:9537380[5]

IDA: Inferred from Direct Assay

F

complete

GO:0042817

pyridoxal metabolic process

PMID:9537380[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0042819

vitamin B6 biosynthetic process

PMID:9537380[5]

IMP: Inferred from Mutant Phenotype

P

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

uidC

PMID:16606699[6]

Experiment(s):EBI-1140332

Protein

glnA

PMID:16606699[6]

Experiment(s):EBI-1140332
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MMKNILAIQS HVVYGHAGNS AAEFPMRRLG ANVWPLNTVQ FSNHTQYGKW TGCVMPPSHL
TEIVQGIAAI DKLHTCDAVL SGYLGSAEQG EHILGIVRQV KAANPQAKYF CDPVMGHPEK
GCIVAPGVAE FHVRHGLPAS DIIAPNLVEL EILCEHAVNN VEEAVLAARE LIAQGPQIVL
VKHLARAGYS RDRFEMLLVT ADEAWHISRP LVDFGMRQPV GVGDVTSGLL LVKLLQGATL
QEALEHVTAA VYEIMVTTKA MQEYELQVVA AQDRIAKPEH YFSATKL
Length

287

Mol. Wt

31.32 kDa

pI

6.5 (calculated)

Extinction coefficient

28,420 - 29,045 (calc based on 8 Y, 3 W, and 5 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

53..268

PF08543 Phosphomethylpyrimidine kinase

PMID:19920124[7]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=pdxY taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129594

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946162

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005475

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77150

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6879

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13940

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946162

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003468

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3699

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 5.3 Yang, Y et al. (1998) Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12. J. Bacteriol. 180 1814-21 PubMed
  6. ↑ 6.0 6.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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