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DNA adenine methylase (EC 2.1.1.72) (DNA-(N(6)-adenine)-methyltransferase) (Deoxyadenosyl-methyltransferase) (M.EcoT4Dam)

 DMA_BPT4                Reviewed;         259 AA.
P04392;
20-MAR-1987, integrated into UniProtKB/Swiss-Prot.
20-MAR-1987, sequence version 1.
30-AUG-2017, entry version 116.
RecName: Full=DNA adenine methylase;
EC=2.1.1.72 {ECO:0000269|PubMed:7782299};
AltName: Full=DNA-(N(6)-adenine)-methyltransferase {ECO:0000303|PubMed:12501249};
AltName: Full=Deoxyadenosyl-methyltransferase;
AltName: Full=M.EcoT4Dam;
Name=DAM;
Enterobacteria phage T4 (Bacteriophage T4).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;
Tevenvirinae; T4virus.
NCBI_TaxID=10665;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6098451;
McDonald P.M., Mosig G.;
"Regulation of a new bacteriophage T4 gene, 69, that spans an origin
of DNA replication.";
EMBO J. 3:2863-2871(1984).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND MUTANT DAMH.
PubMed=2510127; DOI=10.1093/nar/17.20.8149;
Miner Z., Schlagman S.L., Hattman S.;
"Single amino acid changes that alter the DNA sequence specificity of
the DNA-[N6-adenine] methyltransferase (Dam) of bacteriophage T4.";
Nucleic Acids Res. 17:8149-8157(1989).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=12626685; DOI=10.1128/MMBR.67.1.86-156.2003;
Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
"Bacteriophage T4 genome.";
Microbiol. Mol. Biol. Rev. 67:86-156(2003).
[4]
SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, AND CATALYTIC ACTIVITY.
PubMed=7782299; DOI=10.1074/jbc.270.24.14389;
Kossykh V.G., Schlagman S.L., Hattman S.;
"Phage T4 DNA [N6-adenine]methyltransferase. Overexpression,
purification, and characterization.";
J. Biol. Chem. 270:14389-14393(1995).
[5]
FUNCTION.
PubMed=12501249; DOI=10.1074/jbc.M210769200;
Zinoviev V.V., Evdokimov A.A., Malygin E.G., Schlagman S.L.,
Hattman S.;
"Bacteriophage T4 Dam DNA-(N6-adenine)-methyltransferase. Processivity
and orientation to the methylation target.";
J. Biol. Chem. 278:7829-7833(2003).
[6] {ECO:0000244|PDB:1Q0S, ECO:0000244|PDB:1Q0T}
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH
S-ADENOSYL-L-HOMOCYSTEINE, AND SUBUNIT.
PubMed=12937411; DOI=10.1038/nsb973;
Yang Z., Horton J.R., Zhou L., Zhang X.J., Dong A., Zhang X.,
Schlagman S.L., Kossykh V., Hattman S., Cheng X.;
"Structure of the bacteriophage T4 DNA adenine methyltransferase.";
Nat. Struct. Biol. 10:849-855(2003).
[7] {ECO:0000244|PDB:1YF3, ECO:0000244|PDB:1YFJ, ECO:0000244|PDB:1YFL}
X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) IN COMPLEX WITH
S-ADENOSYL-L-HOMOCYSTEINE.
PubMed=15882618; DOI=10.1016/j.cell.2005.02.021;
Horton J.R., Liebert K., Hattman S., Jeltsch A., Cheng X.;
"Transition from nonspecific to specific DNA interactions along the
substrate-recognition pathway of dam methyltransferase.";
Cell 121:349-361(2005).
-!- FUNCTION: Methyltransferase that methylates adenine residues in
the dsDNA sequence GATC. May prevent degradation of viral DNA by
the host restriction-modification antiviral defense system.
{ECO:0000269|PubMed:12501249, ECO:0000305}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + adenine in DNA = S-
adenosyl-L-homocysteine + N-6-methyladenine in DNA.
{ECO:0000269|PubMed:7782299}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.1 uM for S-adenosylmethionine {ECO:0000269|PubMed:7782299};
pH dependence:
Optimum pH is 7.0-8.5. {ECO:0000269|PubMed:7782299};
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12937411,
ECO:0000269|PubMed:7782299}.
-!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
{ECO:0000305}.
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EMBL; X01416; CAA25660.1; -; Genomic_DNA.
EMBL; X17641; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; K03113; AAA32555.1; -; Genomic_DNA.
EMBL; AF158101; AAD42553.1; -; Genomic_DNA.
PIR; A00554; XYBPT4.
RefSeq; NP_049647.1; NC_000866.4.
PDB; 1Q0S; X-ray; 2.30 A; A=1-259.
PDB; 1Q0T; X-ray; 3.10 A; A/B=1-259.
PDB; 1YF3; X-ray; 2.29 A; A/B=1-259.
PDB; 1YFJ; X-ray; 2.69 A; A/B/C/D/E/F=1-259.
PDB; 1YFL; X-ray; 3.09 A; A/B/D/E=1-259.
PDBsum; 1Q0S; -.
PDBsum; 1Q0T; -.
PDBsum; 1YF3; -.
PDBsum; 1YFJ; -.
PDBsum; 1YFL; -.
ProteinModelPortal; P04392; -.
SMR; P04392; -.
DrugBank; DB01752; S-Adenosyl-L-Homocysteine.
REBASE; 2837; M.EcoT4Dam.
GeneID; 1258548; -.
KEGG; vg:1258548; -.
KO; K06223; -.
OrthoDB; VOG0900025E; -.
BRENDA; 2.1.1.72; 732.
EvolutionaryTrace; P04392; -.
Proteomes; UP000009087; Genome.
GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IEA:UniProtKB-EC.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
GO; GO:0099018; P:restriction-modification system evasion by virus; IEA:UniProtKB-KW.
Gene3D; 1.10.1020.10; -; 1.
InterPro; IPR023095; Ade_MeTrfase_dom_2.
InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
InterPro; IPR012263; M_m6A_EcoRV.
InterPro; IPR012327; MeTrfase_D12.
InterPro; IPR029063; SAM-dependent_MTases.
PANTHER; PTHR30481; PTHR30481; 1.
Pfam; PF02086; MethyltransfD12; 1.
PIRSF; PIRSF000398; M_m6A_EcoRV; 1.
PRINTS; PR00505; D12N6MTFRASE.
SUPFAM; SSF53335; SSF53335; 1.
TIGRFAMs; TIGR00571; dam; 1.
PROSITE; PS00092; N6_MTASE; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; DNA replication;
Host-virus interaction; Methyltransferase; Reference proteome;
Restriction-modification system evasion by virus;
S-adenosyl-L-methionine; Transferase.
CHAIN 1 259 DNA adenine methylase.
/FTId=PRO_0000087990.
REGION 32 37 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1Q0T,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
REGION 156 157 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
BINDING 7 7 S-adenosyl-L-methionine.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1Q0T,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
BINDING 11 11 S-adenosyl-L-methionine; via amide
nitrogen. {ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
BINDING 50 50 S-adenosyl-L-methionine.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1Q0T,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
BINDING 171 171 S-adenosyl-L-methionine.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
BINDING 181 181 S-adenosyl-L-methionine.
{ECO:0000244|PDB:1Q0S,
ECO:0000244|PDB:1Q0T,
ECO:0000244|PDB:1YF3,
ECO:0000244|PDB:1YFJ}.
MUTAGEN 126 126 P->S: In damh; hypermethylating mutant.
CONFLICT 139 140 QY -> RF (in Ref. 2; X17641).
{ECO:0000305}.
CONFLICT 209 209 Q -> L (in Ref. 2; X17641).
{ECO:0000305}.
TURN 12 14 {ECO:0000244|PDB:1YF3}.
HELIX 15 20 {ECO:0000244|PDB:1YF3}.
STRAND 26 30 {ECO:0000244|PDB:1YF3}.
HELIX 39 41 {ECO:0000244|PDB:1YF3}.
STRAND 44 49 {ECO:0000244|PDB:1YF3}.
HELIX 53 62 {ECO:0000244|PDB:1YF3}.
HELIX 67 76 {ECO:0000244|PDB:1YF3}.
HELIX 84 97 {ECO:0000244|PDB:1YF3}.
HELIX 100 107 {ECO:0000244|PDB:1YF3}.
HELIX 111 113 {ECO:0000244|PDB:1YF3}.
HELIX 136 146 {ECO:0000244|PDB:1YF3}.
HELIX 147 149 {ECO:0000244|PDB:1YF3}.
STRAND 150 153 {ECO:0000244|PDB:1YF3}.
HELIX 157 159 {ECO:0000244|PDB:1YF3}.
STRAND 166 170 {ECO:0000244|PDB:1YF3}.
STRAND 175 177 {ECO:0000244|PDB:1YFL}.
HELIX 180 184 {ECO:0000244|PDB:1YF3}.
HELIX 187 201 {ECO:0000244|PDB:1YF3}.
TURN 202 204 {ECO:0000244|PDB:1YF3}.
STRAND 206 215 {ECO:0000244|PDB:1YF3}.
HELIX 221 227 {ECO:0000244|PDB:1YF3}.
STRAND 230 234 {ECO:0000244|PDB:1YF3}.
HELIX 237 242 {ECO:0000244|PDB:1YF3}.
STRAND 254 258 {ECO:0000244|PDB:1YF3}.
SEQUENCE 259 AA; 30417 MW; A49401D059A4388D CRC64;
MLGAIAYTGN KQSLLPELKS HFPKYNRFVD LFCGGLSVSL NVNGPVLAND IQEPIIEMYK
RLINVSWDDV LKVIKQYKLS KTSKEEFLKL REDYNKTRDP LLLYVLHFHG FSNMIRINDK
GNFTTPFGKR TINKNSEKQY NHFKQNCDKI IFSSLHFKDV KILDGDFVYV DPPYLITVAD
YNKFWSEDEE KDLLNLLDSL NDRGIKFGQS NVLEHHGKEN TLLKEWSKKY NVKHLNKKYV
FNIYHSKEKN GTDEVYIFN


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