xthA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

xthA

Gene Synonym(s)

ECK1747, b1749, JW1738, xth[1], xth

Product Desc.

exonuclease III[2][3]

Exodeoxyribonuclease III and AP endodeoxyribonuclease VI; RNase H activity; DNA repair[4]

Product Synonyms(s)

exonuclease III[1], B1749[2][1], Xth[2][1], XthA[2][1] , ECK1747, JW1738, xth, b1749

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): xthA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

xthA

Mnemonic

Exonuclease III

Synonyms

ECK1747, b1749, JW1738, xth[1], xth

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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

39.45 minutes 

MG1655: 1830452..1831258
<gbrowseImage> name=NC_000913:1830452..1831258 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1809693..1810499
<gbrowseImage> name=NC_012967:1809693..1810499 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1722511..1723317
<gbrowseImage> name=NC_012759:1722511..1723317 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1834142..1834948
<gbrowseImage> name=NC_007779:1834142..1834948 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1921023..1921829
<gbrowseImage> name=NC_010473:1921023..1921829 source=DH10B preset=GeneLocation </gbrowseImage>

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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

ΔxthA (Keio:JW1738)

deletion

deletion

PMID:16738554

Shigen
CGSC9466[5]

xthA::Tn5KAN-2 (FB20447)

Insertion at nt 308 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20447

contains pKD46

xthA::Tn5KAN-2 (FB20448)

Insertion at nt 308 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20448

does not contain pKD46

xthA14

CGSC:9065

xthA1

CGSC:9923

xthA3

CGSC:13038

xthA15

CGSC:19379

ΔxthA747::kan

PMID:16738554

CGSC:103420


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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

JW1738

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATTTGTCTCTTTTAATAT

Primer 2:CCGCGGCGGAAGGTCGCCCAGAC

5E12

Kohara Phage

Genobase

PMID:3038334

4B8

Kohara Phage

Genobase

PMID:3038334

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 8% [6]
Synonyms:zdh-925::Tn10

zdj-276::Tn10

Linked marker

CAG18464 = CGSC7387[5]

est. P1 cotransduction: 93% [6]
Synonyms:zdi-276::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:EG11073

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11073

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001062

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946254

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1066

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005829

Escherichia coli str. K-12 substr. MG1655

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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

XthA

Synonyms

exonuclease III[1], B1749[2][1], Xth[2][1], XthA[2][1] , ECK1747, JW1738, xth, b1749

Product description

exonuclease III[2][3]

Exodeoxyribonuclease III and AP endodeoxyribonuclease VI; RNase H activity; DNA repair[4]

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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0009314

response to radiation

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000097

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020847

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020848

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004808

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000097

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020847

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020848

F

Seeded from EcoCyc (v14.0)

complete

GO:0004527

exonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000097

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020847

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020848

C

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000097

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004808

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020847

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020848

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0008853

exodeoxyribonuclease III activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.11.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

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

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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

aceE

PMID:15690043

Experiment(s):EBI-890451

Protein

aceF

PMID:15690043

Experiment(s):EBI-890451

Protein

lpdA

PMID:15690043

Experiment(s):EBI-890451

Protein

malP

PMID:15690043

Experiment(s):EBI-890451

Protein

nrdI

PMID:16606699

Experiment(s):EBI-1140692

Protein

yhaJ

PMID:16606699

Experiment(s):EBI-1140692

Protein

fliT

PMID:16606699

Experiment(s):EBI-1140692

Protein

rplF

PMID:16606699

Experiment(s):EBI-1140692

Protein

nuoE

PMID:16606699

Experiment(s):EBI-1140692

Protein

yahB

PMID:16606699

Experiment(s):EBI-1140692

Protein

groL

PMID:16606699

Experiment(s):EBI-1140692

Protein

uspG

PMID:16606699

Experiment(s):EBI-1140692

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1140692
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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 

MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL GYNVFYHGQK
GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL GNVTVINGYF PQGESRDHPI
KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG DMNISPTDLD IGIGEENRKR WLRTGKCSFL
PEEREWMDRL MSWGLVDTFR HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC
CVETGIDYEI RSMEKPSDHA PVWATFRR
Length

268

Mol. Wt

30.969 kDa

pI

6.6 (calculated)

Extinction coefficient

39,420 - 39,795 (calc based on 8 Y, 5 W, and 3 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

1..266

PF03372 Endonuclease/Exonuclease/phosphatase family

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=xthA 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:16129703

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946254

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005829

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P09030

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11073

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11073

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946254

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001062

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1066

Escherichia coli str. K-12 substr. MG1655

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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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

3.68E+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

Ecoli K-12

6.681+/-0.05

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.066377171

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

3914

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

1111

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

2245

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

xthA

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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_000913:1830432..1830472 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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<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:b1749 (EcoliWiki Page)

NCBI GEO profiles for xthA

microarray

GenExpDB:b1749 (EcoliWiki Page)

Summary of data for xthA 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

GFP Fusion

Intergenic region (1829915..1830498) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:D9[7]

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Notes

Accessions Related to xthA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11073

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1066

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1749

EcoGene

EcoGene:EG11073

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001062

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005829

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • ENSANGP00000020924 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT2G41460 (score: 1.000; bootstrap: 72%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000003559 (score: 1.000; bootstrap: 88%)
  • ENSBTAP00000000007 (score: 0.733)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00038070 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00001372 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000008071 (score: 1.000; bootstrap: 86%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016619 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-CDNA-040425-3708 (score: 1.000; bootstrap: 57%)
  • ZDB-GENE-040426-2761 (score: 0.995)
  • ZDB-CDNA-050612-208 (score: 0.925)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0185018 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0004584 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA16470-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000216714 (score: 1.000; bootstrap: 77%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000025143 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000008838 (score: 1.000; bootstrap: 70%)

From Inparanoid:20070104

Mus musculus

  • MGI:88042 (score: 1.000; bootstrap: 73%)

From Inparanoid:20070104

Oryza gramene

  • Q5VQJ9 (score: 1.000; bootstrap: 77%)
  • Q5VQJ8 (score: 0.363)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000010344 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000013176 (score: 1.000; bootstrap: 74%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC3D60 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000136145 (score: 1.000; bootstrap: 70%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00010570001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000027324 (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Shigella flexneri

XTHA

From SHIGELLACYC

E. coli O157

XTHA

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF03372 Endonuclease/Exonuclease/phosphatase family

Panther (EcoliWiki Page)

PTHR22748:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:56219

EcoCyc

EcoCyc:EG11073

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11073

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001062

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1066

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005829

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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