|Gene:||dam||Accession Numbers: EG10204 (EcoCyc), b3387, ECK3374|
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].
|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
|Biological Process:||GO:0006261 - DNA-dependent DNA replication
GO:0006298 - mismatch repair [Lu83, Pukkila83]
GO:0006306 - DNA methylation [Urig02]
GO:0006260 - DNA replication [UniProtGOA11a]
GO:0032259 - methylation [UniProtGOA11a, GOA01a]
GO:0032775 - DNA methylation on adenine [GOA01a]
|Molecular Function:||GO:0003677 - DNA binding
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [GOA01, GOA01a, Herman82]
GO:0003676 - nucleic acid binding [GOA01a]
GO:0008168 - methyltransferase activity [UniProtGOA11a, GOA01a]
GO:0016740 - transferase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||information transfer → DNA related → DNA restriction/modification|
|regulation → type of regulation → DNA structure level → methylation|
|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]|
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: 220.127.116.11
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.
10/20/97 Gene b3387 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10204; confirmed by SwissProt match.
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
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
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
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
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
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
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
Smith85: 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
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
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