pdxK:Gene Product(s)

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

Nomenclature

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Standard name

PdxK

Synonyms

pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase[1], B2418[2][1], PdxL[2][1], ThiJ[2][1], YfeI[2][1], PdxK[2][1] , ECK2413, JW2411, pdxL, thiJ, yfeI, b2418

Product description

PdxK[2][3];

Component of PDXK-CPLX[2]

B6-vitamer kinase; pyridoxine (PN)/pyridoxal (PL)/pyridoxamine (PM) 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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0008478

pyridoxal kinase activity

PMID:4917899[5] PMID:8764513[6]

IMP: Inferred from Mutant Phenotype

F

complete

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:0000287

magnesium ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01638

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0004340

glucokinase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01638

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01638

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_01638

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01638

F

Seeded from EcoCyc (v14.0)

complete

GO:0008478

pyridoxal kinase activity

PMID:16740960[7]

IDA: Inferred from Direct Assay

F

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:0008478

pyridoxal kinase activity

PMID:4917899[5]

IMP: Inferred from Mutant Phenotype

F

Seeded from EcoCyc (v14.0)

complete

GO:0008478

pyridoxal kinase activity

PMID:8764513[6]

IMP: Inferred from Mutant Phenotype

F

Seeded from EcoCyc (v14.0)

complete

GO:0008615

pyridoxine biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004625

P

Seeded from EcoCyc (v14.0)

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

Subunits of PDXK-CPLX

could be indirect

Protein

dnaK

PMID:16606699[8]

Experiment(s):EBI-1142759

Protein

rplQ

PMID:16606699[8]

Experiment(s):EBI-1142759
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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 

MSSLLLFNDK SRALQADIVA VQSQVVYGSV GNSIAVPAIK QNGLNVFAVP TVLLSNTPHY
DTFYGGAIPD EWFSGYLRAL QERDALRQLR AVTTGYMGTA SQIKILAEWL TALRKDHPDL
LIMVDPVIGD IDSGIYVKPD LPEAYRQYLL PLAQGITPNI FELEILTGKN CRDLDSAIAA
AKSLLSDTLK WVVVTSASGN EENQEMQVVV VTADSVNVIS HSRVKTDLKG TGDLFCAQLI
SGLLKGKALT DAVHRAGLRV LEVMRYTQQH ESDELILPPL AEA
Length

283

Mol. Wt

30.847 kDa

pI

5.1 (calculated)

Extinction coefficient

29,910 - 30,160 (calc based on 9 Y, 3 W, and 2 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

47..275

PF08543 Phosphomethylpyrimidine kinase

PMID:19920124[9]

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

Structures

<beststructure> gene=pdxK 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:16130344

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946881

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007973

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P40191

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7259

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12642

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946881

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003833

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2519

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 1.5 1.6 1.7 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 2.4 2.5 2.6 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 White, RS & Dempsey, WB (1970) Purification and properties of vitamin B6 kinase from Escherichia coli B. Biochemistry 9 4057-64 PubMed
  6. ↑ 6.0 6.1 Yang, Y et al. (1996) Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12. FEMS Microbiol. Lett. 141 89-95 PubMed
  7. ↑ Safo, MK et al. (2006) Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases. J. Bacteriol. 188 4542-52 PubMed
  8. ↑ 8.0 8.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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