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Escherichia coli K-12 substr. MG1655 Enzyme: DNA adenine methyltransferase



Gene: dam Accession Numbers: EG10204 (EcoCyc), b3387, ECK3374

Regulation Summary Diagram: ?

Summary:
DNA adenine methyltransferase (Dam), which is responsible for methylation of nearly all GATC sequences in E. coli [Geier79], is encoded by the dam gene and occurs at about 130 molecules per rapidly growing cell [Boye92]. Upon replication of DNA, previously methylated sites become hemimethylated and are therefore targets for Dam. Dam transfers a methyl group from S-adenosyl-L-methionine (AdoMet) to create a N6-methyladenine at the GATC site and S-adenosyl-L-homocysteine. This is accomplished by a base-flipping mechanism in which the target residue is flipped out of the DNA strand into the active site of the enzyme [LobnerOlesen05]. AdoMet also acts as an allosteric effector for binding of Dam to its target sequence [Bergerat90].

Methylation of GATC sites is important for a number of functions including modulation of gene expression and chromosome initiation, nucleoid stabilization, and methyl-directed mismatch repair. The methylation state of gene promoter regions can affect whether transcription of the gene occurs. When base mismatches occur during replication, DNA mismatch repair enzymes repair the unmethylated (new) DNA strand and leave the methylated (old) strand intact. When Dam methylation is blocked, mismatch repair occurs with equal frequency on both the new and old strands, leading to increased mutagenesis and the necessity for repair by recombination [LobnerOlesen05].

SeqA, which binds in the wake of DNA replication, effectively competes with Dam for access to hemimethylated GATC sites [LobnerOlesen05].

DNA methylation by Dam has been shown to occur processively [Urig02].

Dam has also been shown to methylate cytosine residues at position N4 when they are located in base mismatches in the target sequence (GCTC/GATC) [Jeltsch99].

The crystal structure of Dam in a complex with DNA in the presence of S-adenosyl-L-homocysteine has been determined to a resolution of 1.8 Å by X-ray crystallography [Horton06].

Review: [LobnerOlesen05]

Gene Citations: [Lyngstadaas95, Lyngstadaas99]

Locations: cytosol

Map Position: [3,513,099 <- 3,513,935] (75.72 centisomes)
Length: 837 bp / 278 aa

Molecular Weight of Polypeptide: 32.1 kD (from nucleotide sequence), 31 kD (experimental) [Herman82 ]

Unification Links: ASAP:ABE-0011063 , CGSC:881 , DIP:DIP-47948N , EchoBASE:EB0200 , EcoGene:EG10204 , EcoliWiki:b3387 , Mint:MINT-1230150 , ModBase:P0AEE8 , OU-Microarray:b3387 , PortEco:dam , PR:PRO_000022398 , Pride:P0AEE8 , Protein Model Portal:P0AEE8 , RefSeq:NP_417846 , RegulonDB:EG10204 , SMR:P0AEE8 , String:511145.b3387 , UniProt:P0AEE8

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR012263 , InterPro:IN-FAMILY:IPR012327 , InterPro:IN-FAMILY:IPR023095 , PDB:Structure:2G1P , PDB:Structure:2ORE , Pfam:IN-FAMILY:PF02086 , Prints:IN-FAMILY:PR00505 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Messer85, Smith85a]
GO:0006298 - mismatch repair Inferred from experiment [Lu83, Pukkila83]
GO:0006306 - DNA methylation Inferred from experiment [Urig02]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0032775 - DNA methylation on adenine Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Urig02]
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Herman82]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA restriction/modification
regulation type of regulation DNA structure level methylation

Essentiality data for dam knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Enzymatic reaction of: DNA adenine methyltransferase

Synonyms: N-6 adenine-specific DNA methylase, site-specific DNA-methyltransferase (adenine-specific), modification methylase, methylase of restriction-modification system, DNA adenine methylase

EC Number: 2.1.1.72

a DNA adenine + S-adenosyl-L-methionine <=> S-adenosyl-L-homocysteine + a DNA 6-methylaminopurine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
S-adenosyl-L-methionine
12.0
[Bonnist12, BRENDA14]
S-adenosyl-L-methionine
5.6, 12.2
1.2e-4, 2.1e-4, 2.5e-4, 2.8e-4, 0.0012
[Bheemanaik06, BRENDA14]
a DNA adenine
0.023, 0.081
[Coffin08, BRENDA14]
a DNA adenine
0.3
[Bonnist12, BRENDA14]
a DNA adenine
0.003
[Coffin09, BRENDA14]
a DNA adenine
0.023, 0.081
0.0038, 0.015
[Coffin09a, BRENDA14]
a DNA adenine
0.0036, 0.017, 0.026, 0.12, 0.27, 0.8, 0.83, 0.91, 1.0, 7.1
9.6e-5, 0.0041, 0.0053, 0.0056, 0.021, 0.094, 0.1, 0.11, 0.12, 0.14, 0.14, 0.16, 0.17, 0.2, 0.23, 0.25, 0.27, 0.3, 0.32, 0.37, 0.45, 0.58, 0.93
[Bheemanaik06, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 10
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 14
[UniProt10a]
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 54
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 181
[UniProt10a]
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3387 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10204; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bergerat90: Bergerat A, Guschlbauer W (1990). "The double role of methyl donor and allosteric effector of S-adenosyl-methionine for Dam methylase of E. coli." Nucleic Acids Res 18(15);4369-75. PMID: 2201947

Bheemanaik06: Bheemanaik S, Reddy YV, Rao DN (2006). "Structure, function and mechanism of exocyclic DNA methyltransferases." Biochem J 399(2);177-90. PMID: 16987108

Bonnist12: Bonnist EY, Liebert K, Dryden DT, Jeltsch A, Jones AC (2012). "Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding." Biophys Chem 160(1);28-34. PMID: 21962489

Boye92: Boye E, Marinus MG, Lobner-Olesen A (1992). "Quantitation of Dam methyltransferase in Escherichia coli." J Bacteriol 174(5);1682-5. PMID: 1537808

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Coffin08: Coffin SR, Reich NO (2008). "Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences." J Biol Chem 283(29);20106-16. PMID: 18502761

Coffin09: Coffin SR, Reich NO (2009). "Escherichia coli DNA adenine methyltransferase: intrasite processivity and substrate-induced dimerization and activation." Biochemistry 48(31);7399-410. PMID: 19580332

Coffin09a: Coffin SR, Reich NO (2009). "Escherichia coli DNA adenine methyltransferase: the structural basis of processive catalysis and indirect read-out." J Biol Chem 284(27);18390-400. PMID: 19419959

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Geier79: Geier GE, Modrich P (1979). "Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease." J Biol Chem 254(4);1408-13. PMID: 368070

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Herman82: Herman GE, Modrich P (1982). "Escherichia coli dam methylase. Physical and catalytic properties of the homogeneous enzyme." J Biol Chem 257(5);2605-12. PMID: 7037767

Horton06: Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X (2006). "Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase." J Mol Biol 358(2);559-70. PMID: 16524590

Jeltsch99: Jeltsch A, Christ F, Fatemi M, Roth M (1999). "On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4." J Biol Chem 274(28);19538-44. PMID: 10391886

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

LobnerOlesen05: Lobner-Olesen A, Skovgaard O, Marinus MG (2005). "Dam methylation: coordinating cellular processes." Curr Opin Microbiol 8(2);154-60. PMID: 15802246

Lu83: Lu AL, Clark S, Modrich P (1983). "Methyl-directed repair of DNA base-pair mismatches in vitro." Proc Natl Acad Sci U S A 80(15);4639-43. PMID: 6308634

Lyngstadaas95: Lyngstadaas A, Lobner-Olesen A, Boye E (1995). "Characterization of three genes in the dam-containing operon of Escherichia coli." Mol Gen Genet 1995;247(5);546-54. PMID: 7603433

Lyngstadaas99: Lyngstadaas A, Lobner-Olesen A, Grelland E, Boye E (1999). "The gene for 2-phosphoglycolate phosphatase (gph) in Escherichia coli is located in the same operon as dam and at least five other diverse genes." Biochim Biophys Acta 1472(1-2);376-84. PMID: 10572959

Messer85: Messer W, Bellekes U, Lother H (1985). "Effect of dam methylation on the activity of the E. coli replication origin, oriC." EMBO J 4(5);1327-32. PMID: 3891330

Pukkila83: Pukkila PJ, Peterson J, Herman G, Modrich P, Meselson M (1983). "Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli." Genetics 104(4);571-82. PMID: 6225697

Smith85a: Smith DW, Garland AM, Herman G, Enns RE, Baker TA, Zyskind JW (1985). "Importance of state of methylation of oriC GATC sites in initiation of DNA replication in Escherichia coli." EMBO J 4(5);1319-26. PMID: 3891329

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urig02: Urig S, Gowher H, Hermann A, Beck C, Fatemi M, Humeny A, Jeltsch A (2002). "The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction." J Mol Biol 319(5);1085-96. PMID: 12079349

Other References Related to Gene Regulation

LobnerOlesen92a: Lobner-Olesen A, Boye E, Marinus MG (1992). "Expression of the Escherichia coli dam gene." Mol Microbiol 1992;6(13);1841-51. PMID: 1630320

Wu92a: Wu TH, Grelland E, Boye E, Marinus MG (1992). "Identification of a weak promoter for the dam gene of Escherichia coli." Biochim Biophys Acta 1992;1131(1);47-52. PMID: 1581360


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, BIOCYC14B.