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dcm:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

dcm

Gene Synonym(s)

ECK1959, b1961, JW1944, mec[1]

Product Desc.

DNA cytosine methylase[2][3]

DNA cytosine methyltransferase; internal cytosine methylated[4]

Product Synonyms(s)

DNA cytosine methylase[1], B1961[2][1], Mec[2][1], Dcm[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dcm-vsr[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(dcm)    Textpresso(dcm)

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Notes

Method of Mutagenesis: Log-phase cultures of strain GM 1 were treated with Alkylating agent (N-methyl-N-nitro-nitrosoguanidine)[5]


Phenotype Observed: Mutants were tested for S-adenosylmethionine methyltransferase activity by measuring the levels of DNA-cytosine (S-adenosylmethionine and DNA-adenine. The mutants showed reduced or absent activity. Also, deficient in methylcytosine in DNA. [5]


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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

dcm

Mnemonic

DNA cytosine methylation

Synonyms

ECK1959, b1961, JW1944, mec[1]

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Notes

Location(s) and DNA Sequence

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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

43.73 minutes 

MG1655: 2030341..2028923
gbrowse_img.php?coord=2028923..2030341&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2034454..2033036
gbrowse_img.php?coord=2033036..2034454&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2121349..2119931
gbrowse_img.php?coord=2119931..2121349&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 1921406..1922824
gbrowse_img.php?coord=1921406..1922824&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

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

Δdcm (Keio:JW1944)

deletion

deletion

PMID:16738554

Shigen
CGSC9617[6]

dcm-6

PMID:7694036

CGSC:5946

Δdcm-735::kan

PMID:16738554

CGSC:100536


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW1944

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGGAAAATATATCAGTAAC

Primer 2:CCTCGTGAACGTCGGCCATGTTG

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[6]

est. P1 cotransduction: 20% [7]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[6]

est. P1 cotransduction: 77% [7]

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10211

EchoBASE (EcoliWiki Page)

EchoBASE:EB0207

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1961

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2380

EcoGene (EcoliWiki Page)

EcoGene:EG10211

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DCM

CGSC (EcoliWiki Page)

CGSC:874

ASAP (EcoliWikiPage)

ASAP:ABE-0006509


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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

Dcm

Synonyms

DNA cytosine methylase[1], B1961[2][1], Mec[2][1], Dcm[2][1]

Product description

DNA cytosine methylase[2][3]

DNA cytosine methyltransferase; internal cytosine methylated[4]

EC number (for enzymes)
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Notes

Function

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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:0003677

DNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001525

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0003886

DNA (cytosine-5-)-methyltransferase activity

GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.37

F

Seeded from EcoCyc [9]

complete

GO:0006306

DNA methylation

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001525

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0008168

methyltransferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc [9]

complete

GO:0009307

DNA restriction-modification system

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc [9]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [9]

complete

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P06959

F

Seeded from EcoCyc [9]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

amn

PMID:16606699

Experiment(s):EBI-1141506

Protein

rplB

PMID:16606699

Experiment(s):EBI-1141506

Protein

rimK

PMID:16606699

Experiment(s):EBI-1141506

Protein

mukB

PMID:16606699

Experiment(s):EBI-1141506

Protein

yedV

PMID:16606699

Experiment(s):EBI-1141506

Protein

groL

PMID:16606699

Experiment(s):EBI-1141506

Protein

purR

PMID:16606699

Experiment(s):EBI-1141506

Protein

rplA

PMID:15690043

Experiment(s):EBI-894157

Protein

rplC

PMID:15690043

Experiment(s):EBI-894157

Protein

rplM

PMID:15690043

Experiment(s):EBI-894157

Protein

rplU

PMID:15690043

Experiment(s):EBI-894157

Protein

rplV

PMID:15690043

Experiment(s):EBI-894157

Protein

rpsC

PMID:15690043

Experiment(s):EBI-894157

Protein

rpsE

PMID:15690043

Experiment(s):EBI-894157

Protein

rpsG

PMID:15690043

Experiment(s):EBI-894157

Protein

rpsN

PMID:15690043

Experiment(s):EBI-894157

Protein

rpsT

PMID:15690043

Experiment(s):EBI-894157

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MQENISVTDS YSTGNAAQAM LEKLLQIYDV KTLVAQLNGV GENHWSAAIL KRALANDSAW
HRLSEKEFAH LQTLLPKPPA HHPHYAFRFI DLFAGIGGIR RGFESIGGQC VFTSEWNKHA
VRTYKANHYC DPATHHFNED IRDITLSHKE GVSDEAAAEH IRQHIPEHDV LLAGFPCQPF
SLAGVSKKNS LGRAHGFACD TQGTLFFDVV RIIDARRPAM FVLENVKNLK SHDQGKTFRI
IMQTLDELGY DVADAEDNGP DDPKIIDGKH FLPQHRERIV LVGFRRDLNL KADFTLRDIS
ECFPAQRVTL AQLLDPMVEA KYILTPVLWK YLYRYAKKHQ ARGNGFGYGM VYPNNPQSVT
RTLSARYYKD GAEILIDRGW DMATGEKDFD DPLNQQHRPR RLTPRECARL MGFEAPGEAK
FRIPVSDTQA YRQFGNSVVV PVFAAVAKLL EPKIKQAVAL RQQEAQHGRR SR
Length

472

Mol. Wt

53.465 kDa

pI

8.7 (calculated)

Extinction coefficient

49,850 - 50,600 (calc based on 15 Y, 5 W, and 6 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.

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10211-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AED9

PFAM (EcoliWiki Page)

PFAM:PF00145

RefSeq (EcoliWiki Page)

RefSeq:NP_416470


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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

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

Transcription and Transcriptional Regulation

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

Transcription unit(s)

dcm-vsr

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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

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gbrowse_img.php?coord=2030321..2030361&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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b1961 (EcoliWiki Page)

NCBI GEO profiles for dcm

microarray

GenExpDB:b1961 (EcoliWiki Page)

Summary of data for dcm 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (2030263..2030413) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:E11[10]

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Notes

Accessions Related to dcm Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10211

EchoBASE (EcoliWiki Page)

EchoBASE:EB0207

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1961

EcoGene (EcoliWiki Page)

EcoGene:EG10211


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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000020403 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000024696 (score: 0.612)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G25480 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000008432 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041008-138 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000014121 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1274787 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00006202001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DCM

From SHIGELLACYC

E. coli O157

DCM

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00145


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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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 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 Marinus MG & Morris NR (1973) Isolation of deoxyribonucleic acid methylase mutants of Escherichia coli K-12. J Bacteriol 114: 1143-50 PubMed EcoliWiki page
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ 9.0 9.1 9.2 9.3 9.4 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  10. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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