dcm: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

dcm

Gene Synonym(s)

ECK1959, b1961, JW1944, mec[1], mec

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] , ECK1959, JW1944, mec, b1961

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

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

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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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], mec

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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

43.73 minutes 

MG1655: 2030341..2028923
<gbrowseImage> name=NC_000913:2028923..2030341 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1921406..1922824
<gbrowseImage> name=NC_012759:1921406..1922824 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2034454..2033036
<gbrowseImage> name=NC_007779:2033036..2034454 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2121349..2119931
<gbrowseImage> name=NC_010473:2119931..2121349 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

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 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

JW1944

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGGAAAATATATCAGTAAC

Primer 2:CCTCGTGAACGTCGGCCATGTTG

25D8

Kohara Phage

Genobase

PMID:3038334

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.

Database Accession Notes

EcoCyc

EcoCyc:EG10211

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10211

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000205

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946479

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0207

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006509

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

Dcm

Synonyms

DNA cytosine methylase[1], B1961[2][1], Mec[2][1], Dcm[2][1] , ECK1959, JW1944, mec, b1961

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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<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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001525

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018117

F

Seeded from EcoCyc (v14.0)

complete

GO:0003886

DNA (cytosine-5-)-methyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.1.37

F

Seeded from EcoCyc (v14.0)

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001525

P

Seeded from EcoCyc (v14.0)

complete

GO:0006306

DNA methylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018117

P

Seeded from EcoCyc (v14.0)

complete

GO:0008168

methyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0489

F

Seeded from EcoCyc (v14.0)

complete

GO:0009307

DNA restriction-modification system

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

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

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

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6

Protein

ssb

PMID:19402753

MALDI(Z-score):34.014209

Protein

secA

PMID:19402753

MALDI(Z-score):17.971649

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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 

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.

Type Residues Description Notes References

Domain

87..451

PF00145 C-5 cytosine-specific DNA methylase

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=dcm 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:16129907

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946479

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006509

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AED9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10211

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10211

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946479

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000205

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0207

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

E. coli K-12 MG1655

298

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

162

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

169

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)

dcm-vsr

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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_000913:2030321..2030361 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: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 Name Resource Type Description Source Notes

GFP Fusion

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

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:E11[8]

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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.

Database Accession Notes

EcoCyc

EcoCyc:EG10211

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0207

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1961

EcoGene

EcoGene:EG10211

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000205

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006509

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

  • 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

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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)

PF00145 C-5 cytosine-specific DNA methylase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53335

Panther (EcoliWiki Page)

PTHR10629:SF11

EcoCyc

EcoCyc:EG10211

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10211

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000205

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0207

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006509

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. ↑ 1.00 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 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
  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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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