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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	pdxA
Gene Synonym(s)	ECK0053, b0052, JW0051^[1], JW0051
Product Desc.	4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent^[2]^[3] 4-hydroxythreonine-4-phosphate dehydrogenase; fourth step in pyridoxal 5-phosphate biosynthesis; isoniazid resistance; requires divalent cations and NAD(P)+^[4]
Product Synonyms(s)	4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent^[1], B0052^[2]^[1], PdxA^[2]^[1] , ECK0053, JW0051, b0052
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): imp-surA-pdxA^[2], pdxA-rsmA^[2], pdxA-ksgA, pdxA-rsmA-apaGH^[2], pdxA-ksgA-apaG-apaH, surA-pdxA-rsmA-apaGH^[2], surA-pdxA-ksgA-apaGH
Regulation/Activity
Quick Links
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Notes

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Converts 4-hydroxy-L-threonine phosphate (HTP) to 3-amino-2-oxopropyl phosphate.^[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	pdxA
Mnemonic	Pyridoxine
Synonyms	ECK0053, b0052, JW0051^[1], JW0051
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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	1.13 minutes	MG1655: 53416..52427 <gbrowseImage> name=NC_000913:52427..53416 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 57611..56622 <gbrowseImage> name=NC_012967:56622..57611 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 52427..53416 <gbrowseImage> name=NC_012759:52427..53416 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 53416..52427 <gbrowseImage> name=NC_007779:52427..53416 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 53416..52427 <gbrowseImage> name=NC_010473:52427..53416 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
pdxA(del) (Keio:JW0051)	deletion	deletion			PMID:16738554	Shigen CGSC8361^[5]
pdxA6						CGSC:8565
pdxA4						CGSC:11554
pdxA4::Mu						CGSC:11556
pdxA764(del)::kan					PMID:16738554	CGSC:102266
pdxA(del)	deletion	deletion	Auxotrophies	deletion causes biosynthesis of pyridoxine to halt inhibiting growth, figure 1 bottom.	PMID:15094056	Strain History: NU812
pdxA(del)/PDX1	reciprocal transformation	reciprocal transformation	Growth Phenotype	Gene, PDX1, from Cercospora nicotianae incorporated into E. coli will restore pyridoxine biosynthesis that deletion of pdxA halted. Growth rate was severely limited and never reached levels of wild type, Figure 1.	PMID:15094056
pdxA:minimudI lacZ			Growth Phenotype	Mutants with lacZ transcriptional fusion showed expression of pdxA incease in proportion to the growth rate, Fig 2. expression leads to PLP biosynthesis.	PMID:11844765		Strain: NU1187
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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
JW0051	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGTTAAAACCCAACGTGTTGT Primer 2:CCTTGGGTGTTAACAATCATTTT
2F7	Kohara Phage	Genobase	PMID:3038334
4A3	Kohara Phage	Genobase	PMID:3038334
8D2	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 48% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 29% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG10691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000684	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944919	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0685	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000178	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	PdxA
Synonyms	4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent^[1], B0052^[2]^[1], PdxA^[2]^[1] , ECK0053, JW0051, b0052
Product description	4-hydroxy-L-threonine phosphate dehydrogenase, NAD-dependent^[2]^[3] 4-hydroxythreonine-4-phosphate dehydrogenase; fourth step in pyridoxal 5-phosphate biosynthesis; isoniazid resistance; requires divalent cations and NAD(P)+^[4]
EC number (for enzymes)	1.1.1.262^[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: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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00536	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	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:0008615	pyridoxine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00536	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008615	pyridoxine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005255	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:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042823	pyridoxal phosphate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00536	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00536	F	Seeded from EcoCyc (v14.0)	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:0050570	4-hydroxythreonine-4-phosphate dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00536	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050570	4-hydroxythreonine-4-phosphate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005255	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050570	4-hydroxythreonine-4-phosphate dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.262	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0170	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005255	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005255	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
		<input name="field[2]" type="hidden" value="" />		IC: Inferred by Curator	EcoliWiki:dnaX	<input name="field[6]" type="hidden" value="" />		Missing: GO ID, reference
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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
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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 MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML GLPLTLRPYS PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET LARACDGCLN GEFAALITGP VHKGVINDAG IPFTGHTEFF EERSQAKKVV MMLATEELRV ALATTHLPLR DIADAITPAL LHEVIAILHH DLRTKFGIAE PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL NGPLPADTLF QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA LELAGRGKAD VGSFITALNL AIKMIVNTQ
Length	329
Mol. Wt	35.113 kDa
pI	6.3 (calculated)
Extinction coefficient	12,950 - 13,450 (calc based on 5 Y, 1 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
Domain	25..322	PF04166 Pyridoxal phosphate biosynthetic protein PdxA		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=pdxA taxon=562,83333 </beststructure>

Models

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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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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:16128046	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944919	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000178	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P19624	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10691	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944919	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000684	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0685	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 MG1655	275	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	136	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	170	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)
lptD-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH
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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_000913:53396..53436 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:b0052 (EcoliWiki Page)	NCBI GEO profiles for pdxA
microarray	GenExpDB:b0052 (EcoliWiki Page)	Summary of data for pdxA 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 pdxA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10691	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0685	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0052
EcoGene	EcoGene:EG10691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000684	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000178	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
Xenopus tropicalis	ENSXETP00000019505 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PDXA	From SHIGELLACYC
E. coli O157	PDXA	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
Pfam (EcoliWiki Page)	PF04166 Pyridoxal phosphate biosynthetic protein PdxA
Superfamily (EcoliWiki Page)	SUPERFAMILY:53659
EcoCyc	EcoCyc:EG10691	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10691	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000684	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0685	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000178	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 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).

pdxA: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 pdxA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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