dam: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

dam

Gene Synonym(s)

ECK3374, b3387, JW3350[1], JW3350

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] , ECK3374, JW3350, b3387

Function from GO

<GO_nr />

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

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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Dam is a base flipping enzyme.[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

dam

Mnemonic

DNA adenine methylase

Synonyms

ECK3374, b3387, JW3350[1], JW3350

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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

75.72 minutes 

MG1655: 3513935..3513099
<gbrowseImage> name=NC_000913:3513099..3513935 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3444595..3443759
<gbrowseImage> name=NC_012967:3443759..3444595 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3400256..3401092
<gbrowseImage> name=NC_012759:3400256..3401092 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4124503..4125339
<gbrowseImage> name=NC_007779:4124503..4125339 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3611680..3610844
<gbrowseImage> name=NC_010473:3610844..3611680 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

Δdam (Keio:JW3350)

deletion

deletion

PMID:16738554

Shigen

dam::Tn5KAN-I-SceI (FB21147)

Insertion at nt 497 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21147

contains pKD46

dam::Tn5KAN-I-SceI (FB21148)

Insertion at nt 497 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21148

does not contain pKD46

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


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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

JW3350

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGAAAAATCGCGCTTTTTT

Primer 2:CCTTTTTTCGCGGGTGAAACGAC

4D4

Kohara Phage

Genobase

PMID:3038334

6F9

Kohara Phage

Genobase

PMID:3038334

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

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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:EG10204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000198

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947893

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0200

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011063

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

Dam

Synonyms

DNA adenine methylase[1], B3387[2][1], Dam[2][1] , ECK3374, JW3350, b3387

Product description

DNA adenine methylase[2][3]

DNA-(adenine-N6)-methyltransferase[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: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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

F

Seeded from EcoCyc (v14.0)

complete

GO:0006298

mismatch repair

PMID:6308634

IDA: Inferred from Direct Assay

P

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002294

F

Seeded from EcoCyc (v14.0)

complete

GO:0006261

DNA-dependent DNA replication

PMID:3891329 PMID:3891330

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002294

P

Seeded from EcoCyc (v14.0)

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012326

P

Seeded from EcoCyc (v14.0)

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012327

P

Seeded from EcoCyc (v14.0)

complete

GO:0009007

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002294

F

Seeded from EcoCyc (v14.0)

complete

GO:0009007

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012326

F

Seeded from EcoCyc (v14.0)

complete

GO:0009007

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012327

F

Seeded from EcoCyc (v14.0)

complete

GO:0009007

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

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.72

F

Seeded from EcoCyc (v14.0)

complete

GO:0032259

methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002052

P

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-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

Protein

glpD

PMID:19402753

LCMS(ID Probability):99.0

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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 

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)

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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

10..251

PF02086 D12 class N6 adenine-specific DNA methyltransferase

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=dam 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:16131265

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947893

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011063

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AEE8

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10204

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947893

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000198

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0200

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

8.907+/-0.078

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.083133971

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

340

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

128

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

215

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)

dam-rpe-gph-trpS

damX-dam-rpe-gph-trpS

aroKB-damX-dam-rpe-gph-trpS

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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_000913:3513915..3513955 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:b3387 (EcoliWiki Page)

NCBI GEO profiles for dam

microarray

GenExpDB:b3387 (EcoliWiki Page)

Summary of data for dam 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 (3513457..3513667) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:F4[7]

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Notes

Accessions Related to dam Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10204

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0200

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3387

EcoGene

EcoGene:EG10204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000198

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011063

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

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

From Inparanoid:20070104

Shigella flexneri

DAM

From SHIGELLACYC

E. coli O157

DAM

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)

PF02086 D12 class N6 adenine-specific DNA methyltransferase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53335

EcoCyc

EcoCyc:EG10204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000198

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0200

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011063

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 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 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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