xdhA:On One Page
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Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
Quickview | | Gene | | Product(s) | | Expression| | Evolution | | References | |
Quickview
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Standard Name |
xdhA |
---|---|
Gene Synonym(s) |
ECK2862, b2866, JW5462, ygeS[1], ygeS |
Product Desc. |
xanthine dehydrogenase subunit with putative molybdenum cofactor-binding domain[2][3]; Component of xanthine dehydrogenase[3] Probable xanthine dehydrogenase molybdenum-binding subunit; involved in limited purine catabolism[4] |
Product Synonyms(s) |
xanthine dehydrogenase, molybdenum binding subunit[1], B2866[2][1], YgeS[2][1], XdhA[2][1] , ECK2862, JW5462, ygeS, b2866 |
Function from GO |
<GO_nr /> |
Knock-Out Phenotype | |
Regulation/Expression | |
Regulation/Activity | |
Quick Links | |
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Notes
AFMB Structural Genomics target No. 102 (http://afmb.cnrs-mrs.fr/article171.html).[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
Standard name |
xdhA |
---|---|
Mnemonic |
Xanthine dehydrogenase |
Synonyms |
ECK2862, b2866, JW5462, ygeS[1], ygeS |
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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.
Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
---|---|---|---|---|
MG1655 |
64.62 minutes |
MG1655: 2998367..3000625 |
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NC_012967: 2886100..2888358 |
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NC_012759: 2885515..2887773 |
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W3110 |
|
W3110: 2999001..3001259 |
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DH10B: 3092237..3094495 |
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Notes
Sequence Features
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
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 |
---|---|---|---|---|---|---|---|
ΔxdhA (Keio:JW5462) |
deletion |
deletion |
PMID:16738554 |
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ΔxdhA788::kan |
PMID:16738554 |
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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
See Help:Gene_resources for help entering information into the Genetic Resources table.
Resource | Resource Type | Source | Notes/Reference |
---|---|---|---|
JW5462 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCCGCGTCGATGCCATTGCTAA Primer 2:CCAATCAATCCTGCCAGATGGAA | |
Kohara Phage |
PMID:3038334 | ||
Kohara Phage |
PMID:3038334 | ||
Linked marker |
est. P1 cotransduction: 12% [6] | ||
Linked marker |
est. P1 cotransduction: % [6] | ||
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:G7485 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG13049 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120004048 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EchoBASE:EB2861 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0009413 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
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 |
XdhA |
---|---|
Synonyms |
xanthine dehydrogenase, molybdenum binding subunit[1], B2866[2][1], YgeS[2][1], XdhA[2][1] , ECK2862, JW5462, ygeS, b2866 |
Product description |
xanthine dehydrogenase subunit with putative molybdenum cofactor-binding domain[2][3]; Component of xanthine dehydrogenase[3] Probable xanthine dehydrogenase molybdenum-binding subunit; involved in limited purine catabolism[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.
Qualifier | GO ID | GO term name | Reference | Evidence Code | with/from | Aspect | Notes | Status |
---|---|---|---|---|---|---|---|---|
GO:0004854 |
xanthine dehydrogenase activity |
GOA:spec |
IEA: Inferred from Electronic Annotation |
EC:1.17.1.4 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006144 |
purine base metabolic process |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0659 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0006166 |
purine ribonucleoside salvage |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0660 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016491 |
oxidoreductase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000674 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016491 |
oxidoreductase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR008274 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016491 |
oxidoreductase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0560 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0030151 |
molybdenum ion binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0500 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR000674 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR008274 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0055114 |
oxidation reduction |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0560 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016491 |
oxidoreductase activity |
PMID:10986234 |
IMP: Inferred from Mutant Phenotype |
F |
Fig 6. |
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 xanthine dehydrogenase |
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 |
---|---|---|---|---|
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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.
Name | |
---|---|
Sequence |
MRVDAIAKVT GRARYTDDYV MAGMCYAKYV RSPIAHGYAV SINDEQARSL PGVLAIFTWE DVPDIPFATA GHAWTLDENK RDTADRALLT RHVRHHGDAV AIVVARDELT AEKAAQLVSI EWQELPVITT PEAALAEDAA PIHNGGNLLK QSTMSTGNVQ QTIDAADYQV QGHYQTPVIQ HCHMESVTSL AWMEDDSRIT IVSSTQIPHI VRRVVGQALD IPWSCVRVIK PFVGGGFGNK QDVLEEPMAA FLTSKLGGIP VKVSLSREEC FLATRTRHAF TIDGQMGVNR DGTLKGYSLD VLSNTGAYAS HGHSIASAGG NKVAYLYPRC AYAYSSKTCY TNLPSAGAMR GYGAPQVVFA VESMLDDAAT ALGIDPVEIR LRNAAREGDA NPLTGKRIYS AGLPECLEKG RKIFEWEKRR AECQNQQGNL RRGVGVACFS YTSNTWPVGV EIAGARLLMN QDGTINVQSG ATEIGQGADT VFSQMVAETV GVPVSDVRVI STQDTDVTPF DPGAFASRQS YVAAPALRSA ALLLKEKIIA HAAVMLHQSA MNLTLIKGHI VLVERPEEPL MSLKDLAMDA FYHPERGGQL SAESSIKTTT NPPAFGCTFV DLTVDIALCK VTINRILNVH DSGHILNPLL AEGQVHGGMG MGIGWALFEE MIIDAKSGVV RNPNLLDYKM PTMPDLPQLE SAFVEINEPQ SAYGHKSLGE PPIIPVAAAI RNAVKMATGV AINTLPLTPK RLYEEFHLAG LI |
Length |
752 |
Mol. Wt |
81.32 kDa |
pI |
6.3 (calculated) |
Extinction coefficient |
76,780 - 78,155 (calc based on 22 Y, 8 W, and 11 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.
|
<motif_map/> |
Structure
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Structure figures<protect> | ||||||
Notes
Gene Product Resources
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
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
Escherichia coli str. K-12 substr. MG1655 | ||
Escherichia coli str. K-12 substr. MG1655 | ||
ASAP:ABE-0009413 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EcoCyc:G7485 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG13049 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
RegulonDB:ECK120004048 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2861 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
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
Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
---|---|---|---|---|---|---|---|
Protein |
E. coli K-12 MG1655 |
4a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
PMID: 24766808 |
Protein |
E. coli K-12 MG1655 |
8 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
0a |
molecules/cell/generation |
|
Ribosome Profiling |
Low confidence in the sequencing data set. |
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.
|
![]() 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
<protect><gbrowseImage>
name=NC_000913:2998347..2998387
source=MG1655
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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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 |
NCBI GEO profiles for xdhA | |
microarray |
Summary of data for xdhA 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 xdhA Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:G7485 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2861 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG13049 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120004048 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0009413 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
Organism | Homologs (Statistics) | Comments |
---|---|---|
Anopheles gambiae |
|
From Inparanoid:20070104 |
Apis mellifera |
|
From Inparanoid:20070104 |
Arabidopsis thaliana |
|
From Inparanoid:20070104 |
Bos taurus |
|
From Inparanoid:20070104 |
Caenorhabditis briggsae |
|
From Inparanoid:20070104 |
Caenorhabditis elegans |
|
From Inparanoid:20070104 |
Canis familiaris |
|
From Inparanoid:20070104 |
Ciona intestinalis |
|
From Inparanoid:20070104 |
Dictyostelium discoideum |
|
From Inparanoid:20070104 |
Drosophila melanogaster |
|
From Inparanoid:20070104 |
Drosophila pseudoobscura |
|
From Inparanoid:20070104 |
Gallus gallus |
|
From Inparanoid:20070104 |
Homo sapiens |
|
From Inparanoid:20070104 |
Macaca mulatta |
|
From Inparanoid:20070104 |
Monodelphis domestica |
|
From Inparanoid:20070104 |
Mus musculus |
|
From Inparanoid:20070104 |
Pan troglodytes |
|
From Inparanoid:20070104 |
Rattus norvegicus |
|
From Inparanoid:20070104 |
Takifugu rubripes |
|
From Inparanoid:20070104 |
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
Xenopus tropicalis |
|
From Inparanoid:20070104 |
Shigella flexneri |
S3068 |
From SHIGELLACYC |
E. coli O157 |
Z4205 |
From ECOO157CYC |
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Do-It-Yourself Web Tools
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Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase |
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PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain |
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EcoCyc:G7485 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG13049 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120004048 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB2861 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0009413 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
Name | URL | Comments |
---|---|---|
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References
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 1.9 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 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 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).
Categories
- Genes with homologs in Anopheles gambiae
- Genes with homologs in Apis mellifera
- Genes with homologs in Arabidopsis thaliana
- Genes with homologs in Bos taurus
- Genes with homologs in Caenorhabditis briggsae
- Genes with homologs in Caenorhabditis elegans
- Genes with homologs in Canis familiaris
- Genes with homologs in Ciona intestinalis
- Genes with homologs in Dictyostelium discoideum
- Genes with homologs in Drosophila melanogaster
- Genes with homologs in Drosophila pseudoobscura
- Genes with homologs in Gallus gallus
- Genes with homologs in Homo sapiens
- Genes with homologs in Macaca mulatta
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Mus musculus
- Genes with homologs in Pan troglodytes
- Genes with homologs in Rattus norvegicus
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157