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Standard Name	pdxK
Gene Synonym(s)	ECK2413, b2418, JW2411, pdxL, thiJ, yfeI^[1], yfeI
Product Desc.	PdxK^[2]^[3]; Component of PDXK-CPLX^[2] B6-vitamer kinase; pyridoxine (PN)/pyridoxal (PL)/pyridoxamine (PM) kinase^[4]
Product Synonyms(s)	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
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pdxK^[2]
Regulation/Activity
Quick Links
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Notes

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Involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	pdxK
Mnemonic	Pyridoxine
Synonyms	ECK2413, b2418, JW2411, pdxL, thiJ, yfeI^[1], yfeI
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	54.62 minutes	MG1655: 2535259..2534408 <gbrowseImage> name=NC_000913:2534408..2535259 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2465963..2465112 <gbrowseImage> name=NC_012967:2465112..2465963 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2420213..2421064 <gbrowseImage> name=NC_012759:2420213..2421064 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2542683..2541832 <gbrowseImage> name=NC_007779:2541832..2542683 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2627024..2626173 <gbrowseImage> name=NC_010473:2626173..2627024 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔpdxK (Keio:JW2411)	deletion	deletion			PMID:16738554	Shigen CGSC9920^[5]
ΔpdxK::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔpdxK747::kan					PMID:16738554	CGSC:102274
PdxK180			Auxotrophies	Mutation causes pyridoxine synthesis to halt, Figure 3. Mutated strain can be supplemented with alanine, cystine and pyruvate to allow some growth to return, Figure 2. Alanine becomes an inhibitor at concentrations greater than 200 mg/liter, Figure 1.	PMID:4559835		Strain History: WG1229
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2411	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTAGTTTGTTGTTGTTTAA Primer 2:CCTGCTTCCGCCAGCGGCGGCAA
12G2	Kohara Phage	Genobase	PMID:3038334
5F7	Kohara Phage	Genobase	PMID:3038334
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[5]	est. P1 cotransduction: 40% ^[6]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 5% ^[6]
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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
EcoCyc	EcoCyc:G7259	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12642	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003833	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946881	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2519	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007973	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

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)	2.7.1.35^[1]
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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 PMID:8764513	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	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	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0008478	pyridoxal kinase activity	PMID:8764513	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	Experiment(s):EBI-1142759
Protein	rplQ		PMID:16606699	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
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<motif_map/>

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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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	2.89E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1273	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	629	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	750	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
pdxK
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2535239..2535279 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2418 (EcoliWiki Page)	NCBI GEO profiles for pdxK
microarray	GenExpDB:b2418 (EcoliWiki Page)	Summary of data for pdxK from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2535175..2535432) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:C5^[7]
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Notes

Accessions Related to pdxK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7259	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2519	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2418
EcoGene	EcoGene:EG12642	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003833	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007973	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Bos taurus	ENSBTAP00000024203 (score: 1.000; bootstrap: 100%) ENSBTAP00000025706 (score: 0.273)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000015643 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000026076 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000038737 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PDXK	From SHIGELLACYC
E. coli O157	PDXK	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF08543 Phosphomethylpyrimidine kinase
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 ^1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 ^2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pdxK:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to pdxK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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