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On One Page

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Standard Name	uxaA
Gene Synonym(s)	ECK3082, b3091, JW3062, ygjW^[1], ygjW
Product Desc.	D-Altronate hydrolase (hydratase), Fe(2)-requiring; galacturonate branch of hexuronate pathway^[2]
Product Synonyms(s)	altronate hydrolase^[1], B3091^[3]^[1], YgjW^[3]^[1], UxaA^[3]^[1] , ECK3082, JW3062, ygjW, b3091
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): uxaCA^[3]
Regulation/Activity
Quick Links
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Notes

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ExuR regulon. UxaA is paralogous to GarD and contains a conserved CxxS redox motif. The unprocessed tisB pre-mRNA functions as an antisense RNA regulator of uxaA, resulting in cleavage of uxaA mRNA at the antisense site and also reciprocal cleavage and activation of the tisB pre-mRNA (forming the +42 tisB RNA) (Weel-Sneve, 2008).^[2]

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	uxaA
Mnemonic	Utilization of heXuronAte
Synonyms	ECK3082, b3091, JW3062, ygjW^[1], ygjW
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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	69.83 minutes	MG1655: 3241336..3239849 <gbrowseImage> name=NC_000913:3239849..3241336 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3176348..3174861 <gbrowseImage> name=NC_012967:3174861..3176348 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3126997..3128484 <gbrowseImage> name=NC_012759:3126997..3128484 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3241970..3240483 <gbrowseImage> name=NC_007779:3240483..3241970 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3339081..3337594 <gbrowseImage> name=NC_010473:3337594..3339081 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)	Reference	Availability	Comments
ΔuxaA (Keio:JW3062)	deletion	deletion	PMID:16738554	Shigen CGSC10337^[4]
uxaA::Tn5KAN-I-SceI (FB21023)	Insertion at nt 921 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21023	does not contain pKD46
uxaA::Tn5KAN-I-SceI (FB21024)	Insertion at nt 921 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21024	contains pKD46
ΔuxaA781::kan			PMID:16738554	CGSC:103352
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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
JW3062	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAATACATCAAGATCCATGC Primer 2:CCTAGCGTTACGCCGCTTTTGAA
15B3	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: 40% ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: % ^[5] Synonyms:zgj-203::Tn10, zha-203::Tn10
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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:EG12734	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12734	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002375	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947603	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2592	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010164	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	UxaA
Synonyms	altronate hydrolase^[1], B3091^[3]^[1], YgjW^[3]^[1], UxaA^[3]^[1] , ECK3082, JW3062, ygjW, b3091
Product description	D-Altronate hydrolase (hydratase), Fe(2)-requiring; galacturonate branch of hexuronate pathway^[2]
EC number (for enzymes)	4.2.1.7^[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:0008789	altronate dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.7	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	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	References	Evidence
Protein	stfR	PMID:16606699	Experiment(s):EBI-1144792
Protein	pheT	PMID:16606699	Experiment(s):EBI-1144792
Protein	ybcS	PMID:16606699	Experiment(s):EBI-1144792
Protein	lhr	PMID:16606699	Experiment(s):EBI-1144792
Protein	yidR	PMID:19402753	MALDI(Z-score):37.785561
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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 MQYIKIHALD NVAVALADLA EGTEVSVDNQ TVTLRQDVAR GHKFALTDIA KGANVIKYGL PIGYALADIA AGVHVHAHNT RTNLSDLDQY RYQPDFQDLP AQAADREVQI YRRANGDVGV RNELWILPTV GCVNGIARQI QNRFLKETNN AEGTDGVFLF SHTYGCSQLG DDHINTRTML QNMVRHPNAG AVLVIGLGCE NNQVAAFRET LGDIDPERVH FMICQQQDDE IEAGIEHLHQ LYNVMRNDKR EPGKLSELKF GLECGGSDGL SGITANPMLG RFSDYVIANG GTTVLTEVPE MFGAEQLLMD HCRDEATFEK LVTMVNDFKQ YFIAHDQPIY ENPSPGNKAG GITTLEDKSL GCTQKAGSSV VVDVLRYGER LKTPGLNLLS APGNDAVATS ALAGAGCHMV LFSTGRGTPY GGFVPTVKIA TNSELAAKKK HWIDFDAGQL IHGKAMPQLL EEFIDTIVEF ANGKQTCNER NDFRELAIFK SGVTL
Length	495
Mol. Wt	54.092 kDa
pI	5.4 (calculated)
Extinction coefficient	30,370 - 31,495 (calc based on 13 Y, 2 W, and 9 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	References
Domain	104..495	PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus	PMID:19920124
Domain	10..81	PF08666 SAF domain	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=uxaA 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:16130986	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947603	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010164	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P42604	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12734	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12734	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002375	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2592	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	Notes	Reference(s)
Protein	Ecoli K-12	2.327+/-0.049	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.009078682	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	53	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	20	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	28^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	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.

Transcription unit(s)
uxaCA
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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_000913:3241316..3241356 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:b3091 (EcoliWiki Page)	NCBI GEO profiles for uxaA
microarray	GenExpDB:b3091 (EcoliWiki Page)	Summary of data for uxaA 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 uxaA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12734	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2592	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3091
EcoGene	EcoGene:EG12734	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002375	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010164	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
Shigella flexneri	UXAA	From SHIGELLACYC
E. coli O157	UXAA	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)	PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus
Pfam (EcoliWiki Page)	PF08666 SAF domain
EcoCyc	EcoCyc:EG12734	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12734	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002375	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2592	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010164	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 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

uxaA: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 uxaA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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