ygdG:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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Standard name

Exo

Synonyms

exonuclease IX (5'-3' exonuclease)[1], B2798[2][1], YgdG[2][1], Xni[2][1], Exo[2][1] , ECK2793, exo, JW5446, xni, b2798

Product description

exonuclease IX, 3'-5' exonuclease[2][3]

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. 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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002421

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008918

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020045

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020046

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020047

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008918

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020045

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: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:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002421

F

Seeded from EcoCyc (v14.0)

complete

GO:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020046

F

Seeded from EcoCyc (v14.0)

complete

GO:0008409

5'-3' exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020047

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

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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

dnaK

PMID:15690043[4]

Experiment(s):EBI-894844

Protein

rpsB

PMID:15690043[4]

Experiment(s):EBI-894844
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Notes

Localization

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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 

MRGLFPISHP AVACSGIECY PYRLIFKGVI VAVHLLIVDA LNLIRRIHAV QGSPCVETCQ
HALDQLIMHS QPTHAVAVFD DENRSSGWRH QRLPDYKAGR PPMPEELHDE MPALRAAFEQ
RGVPCWSTSG NEADDLAATL AVKVTQAGHQ ATIVSTDKGY CQLLSPTLRI RDYFQKRWLD
APFIDKEFGV QPQQLPDYWG LAGISSSKVP GVAGIGPKSA TQLLVEFQSL EGIYENLDAV
AEKWRKKLET HKEMAFLCRD IARLQTDLHI DGNLQQLRLV R
Length

281

Mol. Wt

31.454 kDa

pI

7.1 (calculated)

Extinction coefficient

37,930 - 38,805 (calc based on 7 Y, 5 W, and 7 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

35..188

PF02739 5'-3' exonuclease, N-terminal resolvase-like domain

PMID:19920124[5]

Domain

190..281

PF01367 5'-3' exonuclease, C-terminal SAM fold

PMID:19920124[5]

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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=ygdG taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

<protect>

</protect>

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:226524743

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947256

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009174

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P38506

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12372

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12372

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947256

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002240

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2275

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  5. ↑ 5.0 5.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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