EcoliHub logo

Try the new EcoliHub and let us know what you'd like to see.

dam:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



See Help:Quickview for help with entering information in the Quickview table.

Standard Name

dam

Gene Synonym(s)

ECK3374, b3387, JW3350[1]

Product Desc.

DNA adenine methylase[2][3]

DNA-(adenine-N6)-methyltransferase[4]

Product Synonyms(s)

DNA adenine methylase[1], B3387[2][1], Dam[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dam-rpe-gph-trpS[2], damX-dam-rpe-gph-trpS[2], aroKB-damX-dam-rpe-gph-trpS[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(dam)    Textpresso(dam)

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]


Dam is a base flipping enzyme.[4]



Gene

[back to top]


Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dam

Mnemonic

DNA adenine methylase

Synonyms

ECK3374, b3387, JW3350[1]

edit table

Notes

Location(s) and DNA Sequence

[back to top]


See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

75.72 minutes 

MG1655: 3513935..3513099
gbrowse_img.php?coord=3513099..3513935&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3444595..3443759
gbrowse_img.php?coord=3443759..3444595&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4124503..4125339
gbrowse_img.php?coord=4124503..4125339&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3611680..3610844
gbrowse_img.php?coord=3610844..3611680&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3400256..3401092
gbrowse_img.php?coord=3400256..3401092&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

edit table

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
edit table

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

Δdam (Keio:JW3350)

deletion

deletion

PMID:16738554

Shigen

dam::Tn5KAN

PMID:12519969

ASAP

At position 497 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB21147

dam::Tn5KAN

PMID:12519969

ASAP

At position 497 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21148

dam-3

CGSC:5949

dam-9(ApR,lac)::MudII301

CGSC:8710

dam-13::Tn9

CGSC:10317

dam-4

CGSC:12884

Δdam-16::KanR

PMID:2854098

CGSC:30826


edit table

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3350

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGAAAAATCGCGCTTTTTT

Primer 2:CCTTTTTTCGCGGGTGAAACGAC

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 71% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 10% [6]
Synonyms:zhg-3086::Tn10, zhh-21::Tn10

edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10204

EchoBASE (EcoliWiki Page)

EchoBASE:EB0200

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3387

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4157

EcoGene (EcoliWiki Page)

EcoGene:EG10204

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DAM

CGSC (EcoliWiki Page)

CGSC:881

ASAP (EcoliWikiPage)

ASAP:ABE-0011063


edit table

Notes

Links

[back to top]



Product(s)

[back to top]



Nomenclature

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

Standard name

Dam

Synonyms

DNA adenine methylase[1], B3387[2][1], Dam[2][1]

Product description

DNA adenine methylase[2][3]

DNA-(adenine-N6)-methyltransferase[4]

EC number (for enzymes)
edit table

Notes

Function

[back to top]


Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0009007

site-specific DNA-methyltransferase (adenine-specific) activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR002294
InterPro:IPR012326
InterPro:IPR012327
EC:2.1.1.72

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [8]

complete

GO:0032259

methylation

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

P

Seeded from EcoCyc [8]

complete

GO:0008168

methyltransferase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR002052
SP_KW:KW-0489

F

Seeded from EcoCyc [8]

complete

GO:0006260

DNA replication

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc [8]

complete

GO:0006306

DNA methylation

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002294
InterPro:IPR012326
InterPro:IPR012327

P

Seeded from EcoCyc [8]

complete

GO:0003677

DNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002294

F

Seeded from EcoCyc [8]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

F

Seeded from EcoCyc [8]

complete

GO:0009007

site-specific DNA-methyltransferase (adenine-specific) activity

PMID:7037767

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0006298

mismatch repair

PMID:6225697

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0006298

mismatch repair

PMID:6308634

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

NOT

GO:0009307

DNA restriction-modification system

P

Seeded from EcoCyc 11.1[3]. Dam methylation is not a component of the E. coli restriction-modification systems, although it does block cleavage in vitro by some Type II restriction endonucleases. Dam functions as a component of methyl-directed mismatch repair.

required field missing

GO:0009007

site-specific DNA-methyltransferase (adenine-specific) activity

PMID:7037767

IDA: Inferred from Direct Assay

F

complete

GO:0006298

mismatch repair

PMID:6225697

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006298

mismatch repair

PMID:6308634

IDA: Inferred from Direct Assay

P

complete

GO:0006261

DNA-dependent DNA replication

PMID:3891329 PMID:3891330

IMP: Inferred from Mutant Phenotype

P

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

aceE

PMID:15690043

Experiment(s):EBI-881035

Protein

lpdA

PMID:15690043

Experiment(s):EBI-881035, EBI-887858

Protein

yjjI

PMID:15690043

Experiment(s):EBI-881035

Protein

glpD

PMID:15690043

Experiment(s):EBI-887858

Protein

rplV

PMID:15690043

Experiment(s):EBI-887858

Protein

serS

PMID:15690043

Experiment(s):EBI-887858

Protein

rplS

PMID:15690043

Experiment(s):EBI-887858

Protein

envY

PMID:16606699

Experiment(s):EBI-1145744

Protein

ulaF

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1145744

Protein

htpG

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpoC

PMID:16606699

Experiment(s):EBI-1145744

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1145744

Protein

ybaB

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpsM

PMID:16606699

Experiment(s):EBI-1145744

Protein

yjbD

PMID:16606699

Experiment(s):EBI-1145744

Protein

narZ

PMID:16606699

Experiment(s):EBI-1145744

Protein

rplD

PMID:16606699

Experiment(s):EBI-1145744

Protein

groL

PMID:16606699

Experiment(s):EBI-1145744

Protein

rplA

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1145744

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1145744

edit table

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
edit table

Notes

Structure and Physical Properties

[back to top]


Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MKKNRAFLKW AGGKYPLLDD IKRHLPKGEC LVEPFVGAGS VFLNTDFSRY ILADINSDLI
SLYNIVKMRT DEYVQAAREL FVPETNCAEV YYQFREEFNK SQDPFRRAVL FLYLNRYGYN
GLCRYNLRGE FNVPFGRYKK PYFPEAELYH FAEKAQNAFF YCESYADSMA RADDASVVYC
DPPYAPLSAT ANFTAYHTNS FTLEQQAHLA EIAEGLVERH IPVLISNHDT MLTREWYQRA
KLHVVKVRRS ISSNGGTRKK VDELLALYKP GVVSPAKK
Length

278

Mol. Wt

32.1 kDa

pI

8.8 (calculated)

Extinction coefficient

40,800 - 41,425 (calc based on 20 Y, 2 W, and 5 C residues)

edit table


Domains/Motifs/Modification Sites

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

TypeResiduesDescriptionNotesReferences
edit table


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

Structures
Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource typeSourceNotes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10204-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AEE8

PFAM (EcoliWiki Page)

PFAM:PF02086

RefSeq (EcoliWiki Page)

RefSeq:NP_417846


edit table

Notes

Links

[back to top]




Expression

[back to top]



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

[back to top]


See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


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

Transcription unit(s)

dam-rpe-gph-trpS

damX-dam-rpe-gph-trpS

aroKB-damX-dam-rpe-gph-trpS

edit table
Figure courtesy of RegulonDB

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

[back to top]


gbrowse_img.php?coord=3513915..3513955&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

[back to top]


Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
edit table


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

TypeReferenceNotes

microarray

GEO Profiles:b3387 (EcoliWiki Page)

NCBI GEO profiles for dam

microarray

GenExpDB:b3387 (EcoliWiki Page)

Summary of data for dam from multiple microarray studies

edit table


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

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (3513457..3513667) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:F4[9]

edit table

Notes

Accessions Related to dam Expression

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10204

EchoBASE (EcoliWiki Page)

EchoBASE:EB0200

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3387

EcoGene (EcoliWiki Page)

EcoGene:EG10204


edit table

Notes

Links

[back to top]



Evolution

[back to top]



Homologs in Other Organisms

[back to top]


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

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000000991 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DAM

From SHIGELLACYC

E. coli O157

DAM

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

Notes

Families

[back to top]


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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02086


edit table

Notes

Links

[back to top]



References

[back to top]


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 1.8 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 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 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. ↑ 7.0 7.1 7.2 7.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/dam:On_One_Page"
Personal tools