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pdxA:On One Page

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Standard Name

pdxA

Gene Synonym(s)

ECK0053, b0052, JW0051[1]

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]

Function from GO
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

DNA display    Protein display    Pubmed(pdxA)    Textpresso(pdxA)

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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]

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Notes

Location(s) and DNA Sequence

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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.13 minutes 

MG1655: 53416..52427
gbrowse_img.php?coord=52427..53416&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 57611..56622
gbrowse_img.php?coord=56622..57611&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 53416..52427
gbrowse_img.php?coord=52427..53416&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 53416..52427
gbrowse_img.php?coord=52427..53416&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 52427..53416
gbrowse_img.php?coord=52427..53416&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔpdxA (Keio:JW0051)

deletion

deletion

PMID:16738554

Shigen
CGSC8361[5]

pdxA6

CGSC:8565

pdxA4

CGSC:11554

pdxA4::Mu

CGSC:11556

ΔpdxA764::kan

PMID:16738554

CGSC:102266


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW0051

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTTAAAACCCAACGTGTTGT

Primer 2:CCTTGGGTGTTAACAATCATTTT

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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10691

EchoBASE (EcoliWiki Page)

EchoBASE:EB0685

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0052

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0065

EcoGene (EcoliWiki Page)

EcoGene:EG10691

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PDXA

CGSC (EcoliWiki Page)

CGSC:420

ASAP (EcoliWikiPage)

ASAP:ABE-0000178


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Notes

Links

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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]

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)
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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0000287

magnesium ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0008270

zinc ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc [7]

complete

GO:0008615

pyridoxine biosynthetic process

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005255
SP_KW:KW-0664
HAMAP:MF_00536

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0016491

oxidoreductase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc [7]

complete

GO:0042823

pyridoxal phosphate biosynthetic process

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00536

P

Seeded from EcoCyc [7]

complete

GO:0046872

metal ion binding

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479
HAMAP:MF_00536

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0050570

4-hydroxythreonine-4-phosphate dehydrogenase activity

GO_REF:0000002
GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005255
EC:1.1.1.262
HAMAP:MF_00536

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0050897

cobalt ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc [7]

complete

GO:0051287

NAD or NADH binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005255

F

Seeded from EcoCyc [7]

complete

GO:0055114

oxidation reduction

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc [7]

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 TypePartnerNotesReferencesEvidence
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

cytoplasm

From EcoCyc[3]


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Notes

Structure and Physical Properties

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

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.

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:PDXA-MONOMER

UniProt (EcoliWiki Page)

UniProt:P19624

PFAM (EcoliWiki Page)

PFAM:PF04166

RefSeq (EcoliWiki Page)

RefSeq:NP_414594


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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

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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gbrowse_img.php?coord=53396..53436&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

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 NameResource TypeDescriptionSourceNotes
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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10691

EchoBASE (EcoliWiki Page)

EchoBASE:EB0685

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0052

EcoGene (EcoliWiki Page)

EcoGene:EG10691


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Notes

Links

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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.

OrganismHomologs (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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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF04166


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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 1.8 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 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 8.2 8.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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