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Product(s) |

Expression|

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Standard Name	pdxJ
Gene Synonym(s)	ECK2562, b2564, JW2548^[1], JW2548
Product Desc.	pyridoxine 5'-phosphate synthase^[2]^[3]; Component of pyridoxine 5'-phosphate synthase^[3] Pyridoxine 5'-phosphate (PNP) synthase; homo-octamer^[4]
Product Synonyms(s)	pyridoxine 5'-phosphate synthase^[1], B2564^[2]^[1], PdxJ^[2]^[1] , ECK2562, JW2548, b2564
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pdxJ-acpS^[2], rnc-era-recO-pdxJ-acpS^[2]
Regulation/Activity
Quick Links
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Notes

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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	pdxJ
Mnemonic	Pyridoxine
Synonyms	ECK2562, b2564, JW2548^[1], JW2548
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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	58.17 minutes, 58.17 minutes	MG1655: 2699751..2699020 <gbrowseImage> name=NC_000913:2699020..2699751 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2623221..2622490 <gbrowseImage> name=NC_012967:2622490..2623221 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2584825..2585556 <gbrowseImage> name=NC_012759:2584825..2585556 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2700385..2699654 <gbrowseImage> name=NC_007779:2699654..2700385 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2791516..2790785 <gbrowseImage> name=NC_010473:2790785..2791516 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
Coding Start (SO:0000323)	MG1655	2699023	Edman degradation	PMID:1537799
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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
ΔpdxJ (Keio:JW2548)	deletion	deletion			PMID:16738554	Shigen CGSC10027^[5]
pdxJG194S		G194S		(in pdxH null mutation suppressor)			Strain variation; seeded from UniProt:P0A794
pdxJ19						CGSC:11583
pdxJ20(ts)			Growth Phenotype	temperature sensitive		CGSC:14597
ΔpdxJ736::kan					PMID:16738554	CGSC:102272
pdxJ8::ΔTn10			Auxotrophies	Insertion of (A8) mutation causes dependency of pyridoxine for growth, Table 4.	PMID:1537799		Strain History: W3110
ΔpdxJ	deletion	deletion	Auxotrophies	Deletion causes pyridoxine synthesis to halt causing growth to halt. Figure 1.	PMID:15094056	Strain History: TX1918

ΔpdxJ/PDX1	Reciprocal transformation	Reciprocal transformation	Growth Phenotype	Gene, PDX1, from Cercospora nicotianae incorporated into E. coli will restore pyridoxine biosynthesis that deletion of pdxJ halted. Growth rate was slower, Figure 1.	PMID:15094056
pdxJ-G194S	Single G-To-A transition at nt 2230 in "pdxJ". (Used the numbering in Lam et al. 1992.^[6]	Singe amino acid change of glycine to serine at position 194 in the pdxJ polypeptide chain	Null Bypass Mutation	The pdxJ-S194G mutation enables the growth of ΔpdxH::ΩCm^R without pyridoxal (see text on pg 2446).	PMID:8636054
pdxJ::mini-mud	Insertions 3 to 5 in figure 2.		Auxotrophies	Insertion mutation inhibited growth of the mutant strain. Insertions 3 to 5 in Figure 2.	PMID:1537800
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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
JW2548	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTGAATTACTGTTAGGCGT Primer 2:CCGCCACGCGCTTCCAGCATCAG
7G4	Kohara Phage	Genobase	PMID:3038334
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 23% ^[7] Synonyms:zff-208::Tn10
nadB51::Tn10	Linked marker	CAG18480 = CGSC7419^[5]	est. P1 cotransduction: 70% ^[7]
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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:EG10693	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000685	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947039	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0687	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008435	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	PdxJ	PdxJ
Synonyms	pyridoxine 5'-phosphate synthase^[1], B2564^[2]^[1], PdxJ^[2]^[1] , ECK2562, JW2548, b2564	pyridoxine 5'-phosphate synthase^[1], B2564^[2]^[1], PdxJ^[2]^[1]
Product description	pyridoxine 5'-phosphate synthase^[2]^[3]; Component of pyridoxine 5'-phosphate synthase^[3] Pyridoxine 5'-phosphate (PNP) synthase; homo-octamer^[4]	pyridoxine 5'-phosphate synthase^[2]^[3]; Component of pyridoxine 5'-phosphate synthase^[3]
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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00279	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004569	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0664	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016769	transferase activity, transferring nitrogenous groups	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00279	F	Seeded from EcoCyc (v14.0)	complete
	GO:0033856	pyridoxine 5'-phosphate synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.99.2	F	Seeded from EcoCyc (v14.0)	complete
	pyridoxine biosynthetic process	<input name="field[2]" type="hidden" value="" />				<input name="field[6]" type="hidden" value="" />		Missing: Valid GO ID, evidence, reference
	GO:0008615	pyridoxine biosynthetic process	PMID:1537799	IMP: Inferred from Mutant Phenotype		P	Table $	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	amiA		PMID:16606699	Experiment(s):EBI-1143283
Protein	xylF		PMID:16606699	Experiment(s):EBI-1143283
Protein	Subunits of pyridoxine 5'-phosphate synthase	could be indirect
Protein	Subunits of pyridoxine 5'-phosphate synthase	could be indirect
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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
cytoplasm			From EcoCyc^[3]
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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 MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE VTTEGGLDVA GQRDKMRDAC KRLADAGIQV SLFIDADEEQ IKAAAEVGAP FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT FAASLGLKVN AGHGLTYHNV KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE ARG
Length	243
Mol. Wt	26.384 kDa
pI	5.9 (calculated)
Extinction coefficient	4,470 - 4,970 (calc based on 3 Y, 0 W, and 4 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
Initiator Methionine	1	Removed	UniProt:P0A794
Domain	4..240	PF03740 Pyridoxal phosphate biosynthesis protein PdxJ		PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=pdxJ 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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Resource type	Source	Notes/Reference
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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:16130489	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947039	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008435	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A794	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10693	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10693	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947039	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000685	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0687	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	7.37E+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	1846	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	1057	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	1463	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)
pdxJ-acpS
rnc-era-recO-pdxJ-acpS
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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_000913:2699731..2699771 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:b2564 (EcoliWiki Page)	NCBI GEO profiles for pdxJ
microarray	GenExpDB:b2564 (EcoliWiki Page)	Summary of data for pdxJ 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
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Notes

Accessions Related to pdxJ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10693	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0687	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2564
EcoGene	EcoGene:EG10693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000685	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008435	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
Anopheles gambiae	ENSANGP00000002017 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PDXJ	From SHIGELLACYC
E. coli O157	PDXJ	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:63892
Pfam (EcoliWiki Page)	PF03740 Pyridoxal phosphate biosynthesis protein PdxJ
EcoCyc	EcoCyc:EG10693	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000685	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0687	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008435	Escherichia coli str. K-12 substr. MG1655
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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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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
↑ Lam, HM et al. (1992) Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations. J. Bacteriol. 174 1554-67 PubMed
↑ ^7.0 ^7.1 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).

pdxJ:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

Notes

Genetic Interactions

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Genetic Resources

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Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

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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 pdxJ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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