sbcC: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

sbcC

Gene Synonym(s)

ECK0391, b0397, JW0387, rmuA[1], rmuA

Product Desc.

ATP-dependent dsDNA exonuclease[2][3];

Component of SbcCD ATP-dependent dsDNA exonuclease[3]

DNA hairpin dsDNA 3'-exonuclease SbcCD, Mn(2+), ATP-dependent; ATP-independent 5' ssDNA endonuclease; required for recombinational repair of dsDNA breaks; cosuppressor with sbcB of recB recC mutations; heterodimeric[4]

Product Synonyms(s)

exonuclease, dsDNA, ATP-dependent[1], B0397[2][1], SbcC[2][1] , ECK0391, JW0387, rmuA, b0397

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sbcC[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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SbcCD can cleave dsDNA 5' ends sealed by a hairpin or by covalent linko a protein. SbcCD limits recombination between short inverted repeats, but is also reported to be required for palindrome-stimulated deletion. SbcCD protein forms a large 1.2 megadalton complex. Second amino acid was sequenced in protein as Gly, but in all DNA samples is a Lys codon. Coiled coil protein.[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

sbcC

Mnemonic

Suppression of recBC

Synonyms

ECK0391, b0397, JW0387, rmuA[1], rmuA

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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

8.88 minutes 

MG1655: 414977..411831
<gbrowseImage> name=NC_000913:411831..414977 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 384176..381030
<gbrowseImage> name=NC_012967:381030..384176 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 314590..317736
<gbrowseImage> name=NC_012759:314590..317736 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 414977..411831
<gbrowseImage> name=NC_007779:411831..414977 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 354308..351162
<gbrowseImage> name=NC_010473:351162..354308 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

Coding Start (SO:0000323)

MG1655

411831

Edman degradation

PMID:9242643


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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

sbcC(del) (Keio:JW0387)

deletion

deletion

PMID:16738554

Shigen
CGSC8563[5]

sbcC761(del)::kan

PMID:16738554

CGSC:102878


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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

JW0387

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAATTCTCAGCCTGCGCCT

Primer 2:CCTTTCACTGCAAACGTACTTTC

6A12

Kohara Phage

Genobase

PMID:3038334

9G9

Kohara Phage

Genobase

PMID:3038334

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[5]

est. P1 cotransduction: 54% [6]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[5]

est. P1 cotransduction: 49% [6]

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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:EG10927

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10927

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000916

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949076

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0920

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001381

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

SbcC

Synonyms

exonuclease, dsDNA, ATP-dependent[1], B0397[2][1], SbcC[2][1] , ECK0391, JW0387, rmuA, b0397

Product description

ATP-dependent dsDNA exonuclease[2][3];

Component of SbcCD ATP-dependent dsDNA exonuclease[3]

DNA hairpin dsDNA 3'-exonuclease SbcCD, Mn(2+), ATP-dependent; ATP-independent 5' ssDNA endonuclease; required for recombinational repair of dsDNA breaks; cosuppressor with sbcB of recB recC mutations; heterodimeric[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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004527

exonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004592

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:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006259

DNA metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004592

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0233

P

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

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 SbcCD ATP-dependent dsDNA exonuclease

could be indirect

Protein

ynbC

PMID:15690043

Experiment(s):EBI-879066

Protein

prs

PMID:16606699

Experiment(s):EBI-1136452

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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

MKILSLRLKN LNSLKGEWKI DFTREPFASN GLFAITGPTG AGKTTLLDAI CLALYHETPR
LSNVSQSQND LMTRDTAECL AEVEFEVKGE AYRAFWSQNR ARNQPDGNLQ VPRVELARCA
DGKILADKVK DKLELTATLT GLDYGRFTRS MLLSQGQFAA FLNAKPKERA ELLEELTGTE
IYGQISAMVF EQHKSARTEL EKLQAQASGV TLLTPEQVQS LTASLQVLTD EEKQLITAQQ
QEQQSLNWLT RQDELQQEAS RRQQALQQAL AEEEKAQPQL AALSLAQPAR NLRPHWERIA
EHSAALAHIR QQIEEVNTRL QSTMALRASI RHHAAKQSAE LQQQQQSLNT WLQEHDRFRQ
WNNEPAGWRA QFSQQTSDRE HLRQWQQQLT HAEQKLNALA AITLTLTADE VATALAQHAE
QRPLRQHLVA LHGQIVPQQK RLAQLQVAIQ NVTQEQTQRN AALNEMRQRY KEKTQQLADV
KTICEQEARI KTLEAQRAQL QAGQPCPLCG STSHPAVEAY QALEPGVNQS RLLALENEVK
KLGEEGATLR GQLDAITKQL QRDENEAQSL RQDEQALTQQ WQAVTASLNI TLQPLDDIQP
WLDAQDEHER QLRLLSQRHE LQGQIAAHNQ QIIQYQQQIE QRQQLLLTTL TGYALTLPQE
DEEESWLATR QQEAQSWQQR QNELTALQNR IQQLTPILET LPQSDELPHC EETVVLENWR
QVHEQCLALH SQQQTLQQQD VLAAQSLQKA QAQFDTALQA SVFDDQQAFL AALMDEQTLT
QLEQLKQNLE NQRRQAQTLV TQTAETLAQH QQHRPDDGLA LTVTVEQIQQ ELAQTHQKLR
ENTTSQGEIR QQLKQDADNR QQQQTLMQQI AQMTQQVEDW GYLNSLIGSK EGDKFRKFAQ
GLTLDNLVHL ANQQLTRLHG RYLLQRKASE ALEVEVVDTW QADAVRDTRT LSGGESFLVS
LALALALSDL VSHKTRIDSL FLDEGFGTLD SETLDTALDA LDALNASGKT IGVISHVEAM
KERIPVQIKV KKINGLGYSK LESTFAVK
Length

1,048

Mol. Wt

118.72 kDa

pI

5.5 (calculated)

Extinction coefficient

98,890 - 99,890 (calc based on 11 Y, 15 W, and 8 C residues)


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

<motif_map/>

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

Structures

<beststructure> gene=sbcC 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:16128382

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949076

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001381

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P13458

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10927

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10927

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949076

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000916

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0920

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

Ecoli K-12

3.02+/-0.066

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.008423395

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

135

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

59

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

66

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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)

sbcC

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_000913:414957..414997 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


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

Type Reference Notes

microarray

GEO Profiles:b0397 (EcoliWiki Page)

NCBI GEO profiles for sbcC

microarray

GenExpDB:b0397 (EcoliWiki Page)

Summary of data for sbcC from multiple microarray studies


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 sbcC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10927

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0920

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0397

EcoGene

EcoGene:EG10927

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000916

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001381

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000025304 (score: 1.000; bootstrap: 73%)
  • ENSANGP00000009410 (score: 0.345)
  • ENSANGP00000013163 (score: 0.130)
  • ENSANGP00000028462 (score: 0.101)
  • ENSANGP00000029072 (score: 0.087)
  • ENSANGP00000012395 (score: 0.081)
  • ENSANGP00000026915 (score: 0.079)
  • ENSANGP00000012515 (score: 0.076)
  • ENSANGP00000014553 (score: 0.069)
  • ENSANGP00000012681 (score: 0.067)
  • ENSANGP00000003753 (score: 0.054)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G48600 (score: 1.000; bootstrap: 70%)
  • AT3G54670 (score: 0.110)
  • AT5G62410 (score: 0.068)
  • AT3G47460 (score: 0.066)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00028930 (score: 1.000; bootstrap: 51%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00003367 (score: 1.000; bootstrap: 59%)
  • WBGene00004873 (score: 0.063)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000019358 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000019902 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000019916 (score: 0.976)
  • ENSCINP00000002997 (score: 0.095)
  • ENSCINP00000019026 (score: 0.072)
  • ENSCINP00000001565 (score: 0.068)
  • ENSCINP00000016764 (score: 0.066)
  • ENSCINP00000000142 (score: 0.054)
  • ENSCINP00000000143 (score: 0.051)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030408-4 (score: 1.000; bootstrap: 65%)
  • ZDB-CDNA-040425-456 (score: 0.898)
  • ZDB-GENE-030429-36 (score: 0.064)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0029688 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000025260 (score: 1.000; bootstrap: 64%)
  • ENSGALP00000013963 (score: 0.084)
  • ENSGALP00000015535 (score: 0.052)

From Inparanoid:20070104

Mus musculus

  • MGI:3045962 (score: 1.000; bootstrap: 73%)
  • MGI:3529431 (score: 0.200)
  • MGI:108084 (score: 0.094)

From Inparanoid:20070104

Oryza gramene

  • Q7F099 (score: 1.000; bootstrap: 50%)
  • Q84VF9 (score: 0.599)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000046513 (score: 1.000; bootstrap: 62%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000046012 (score: 1.000; bootstrap: 72%)
  • ENSRNOP00000029356 (score: 0.121)
  • ENSRNOP00000012373 (score: 0.059)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YFR031C (score: 1.000; bootstrap: 66%)
  • YJL074C (score: 0.093)
  • YFL008W (score: 0.075)
  • YLR086W (score: 0.070)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC14864c (score: 1.000; bootstrap: 100%)
  • SPCC1628c (score: 0.081)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000156381 (score: 1.000; bootstrap: 72%)
  • NEWSINFRUP00000157894 (score: 0.517)
  • NEWSINFRUP00000174922 (score: 0.507)
  • NEWSINFRUP00000163156 (score: 0.507)
  • NEWSINFRUP00000180129 (score: 0.497)
  • NEWSINFRUP00000143265 (score: 0.488)
  • NEWSINFRUP00000179462 (score: 0.483)
  • NEWSINFRUP00000151248 (score: 0.481)
  • NEWSINFRUP00000132857 (score: 0.444)
  • NEWSINFRUP00000150658 (score: 0.361)
  • NEWSINFRUP00000168713 (score: 0.243)
  • NEWSINFRUP00000163074 (score: 0.241)
  • NEWSINFRUP00000173334 (score: 0.217)
  • NEWSINFRUP00000163073 (score: 0.215)
  • NEWSINFRUP00000148968 (score: 0.208)
  • NEWSINFRUP00000161111 (score: 0.198)
  • NEWSINFRUP00000179678 (score: 0.159)
  • NEWSINFRUP00000166748 (score: 0.156)
  • NEWSINFRUP00000178792 (score: 0.144)
  • NEWSINFRUP00000172455 (score: 0.138)
  • NEWSINFRUP00000177516 (score: 0.101)
  • NEWSINFRUP00000163147 (score: 0.100)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000040488 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Shigella flexneri

SBCC

From SHIGELLACYC

E. coli O157

SBCC

From ECOO157CYC


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

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR18937:SF1

EcoCyc

EcoCyc:EG10927

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10927

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000916

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0920

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001381

Escherichia coli str. K-12 substr. MG1655

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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 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 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 3.3 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).

Categories

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