DMA_BPT4
ID DMA_BPT4 Reviewed; 259 AA.
AC P04392;
DT 20-MAR-1987, integrated into UniProtKB/Swiss-Prot.
DT 20-MAR-1987, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=DNA adenine methylase;
DE EC=2.1.1.72 {ECO:0000269|PubMed:2510127, ECO:0000269|PubMed:7782299};
DE AltName: Full=DNA-(N(6)-adenine)-methyltransferase {ECO:0000303|PubMed:12501249};
DE AltName: Full=Deoxyadenosyl-methyltransferase;
DE AltName: Full=Orphan methyltransferase M.EcoT4Dam {ECO:0000303|PubMed:12654995};
DE Short=M.EcoT4Dam {ECO:0000303|PubMed:12654995};
GN Name=DAM {ECO:0000303|PubMed:2510127};
OS Enterobacteria phage T4 (Bacteriophage T4).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Tequatrovirus.
OX NCBI_TaxID=10665;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6098451; DOI=10.1002/j.1460-2075.1984.tb02221.x;
RA McDonald P.M., Mosig G.;
RT "Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA
RT replication.";
RL EMBO J. 3:2863-2871(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, MUTANT
RP DAMH, AND MUTAGENESIS OF PRO-126 AND PHE-127.
RX PubMed=2510127; DOI=10.1093/nar/17.20.8149;
RA Miner Z., Schlagman S.L., Hattman S.;
RT "Single amino acid changes that alter the DNA sequence specificity of the
RT DNA-[N6-adenine] methyltransferase (Dam) of bacteriophage T4.";
RL Nucleic Acids Res. 17:8149-8157(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12626685; DOI=10.1128/mmbr.67.1.86-156.2003;
RA Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
RT "Bacteriophage T4 genome.";
RL Microbiol. Mol. Biol. Rev. 67:86-156(2003).
RN [4]
RP SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, AND CATALYTIC ACTIVITY.
RX PubMed=7782299; DOI=10.1074/jbc.270.24.14389;
RA Kossykh V.G., Schlagman S.L., Hattman S.;
RT "Phage T4 DNA [N6-adenine]methyltransferase. Overexpression, purification,
RT and characterization.";
RL J. Biol. Chem. 270:14389-14393(1995).
RN [5]
RP NOMENCLATURE, AND SUBTYPE.
RX PubMed=12654995; DOI=10.1093/nar/gkg274;
RA Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A.,
RA Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K.,
RA Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S.,
RA Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A.,
RA Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S.,
RA Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V.,
RA Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E.,
RA Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W.,
RA Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.;
RT "A nomenclature for restriction enzymes, DNA methyltransferases, homing
RT endonucleases and their genes.";
RL Nucleic Acids Res. 31:1805-1812(2003).
RN [6]
RP FUNCTION.
RX PubMed=12501249; DOI=10.1074/jbc.m210769200;
RA Zinoviev V.V., Evdokimov A.A., Malygin E.G., Schlagman S.L., Hattman S.;
RT "Bacteriophage T4 Dam DNA-(N6-adenine)-methyltransferase. Processivity and
RT orientation to the methylation target.";
RL J. Biol. Chem. 278:7829-7833(2003).
RN [7] {ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1Q0T}
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, AND SUBUNIT.
RX PubMed=12937411; DOI=10.1038/nsb973;
RA Yang Z., Horton J.R., Zhou L., Zhang X.J., Dong A., Zhang X.,
RA Schlagman S.L., Kossykh V., Hattman S., Cheng X.;
RT "Structure of the bacteriophage T4 DNA adenine methyltransferase.";
RL Nat. Struct. Biol. 10:849-855(2003).
RN [8] {ECO:0007744|PDB:1YF3, ECO:0007744|PDB:1YFJ, ECO:0007744|PDB:1YFL}
RP X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE.
RX PubMed=15882618; DOI=10.1016/j.cell.2005.02.021;
RA Horton J.R., Liebert K., Hattman S., Jeltsch A., Cheng X.;
RT "Transition from nonspecific to specific DNA interactions along the
RT substrate-recognition pathway of dam methyltransferase.";
RL Cell 121:349-361(2005).
CC -!- FUNCTION: An alpha subtype methylase, recognizes the double-stranded
CC sequence 5'-GATC-3' and methylates A-2. Also acts on 5-
CC hydroxymethylcytosine (hmC)-containing DNA, the normal base in this
CC virus (PubMed:12654995, PubMed:2510127). May prevent degradation of
CC viral DNA by the host restriction-modification antiviral defense system
CC (Probable). {ECO:0000269|PubMed:12501249, ECO:0000269|PubMed:2510127,
CC ECO:0000303|PubMed:12654995, ECO:0000305, ECO:0000305|PubMed:2510127}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an
CC N(6)-methyl-2'-deoxyadenosine in DNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:15197, Rhea:RHEA-COMP:12418, Rhea:RHEA-
CC COMP:12419, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:90615, ChEBI:CHEBI:90616; EC=2.1.1.72;
CC Evidence={ECO:0000269|PubMed:2510127, ECO:0000269|PubMed:7782299};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.1 uM for S-adenosylmethionine {ECO:0000269|PubMed:7782299};
CC pH dependence:
CC Optimum pH is 7.0-8.5. {ECO:0000269|PubMed:7782299};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12937411,
CC ECO:0000269|PubMed:7782299}.
CC -!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
CC {ECO:0000305}.
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DR EMBL; X01416; CAA25660.1; -; Genomic_DNA.
DR EMBL; X17641; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; K03113; AAA32555.1; -; Genomic_DNA.
DR EMBL; AF158101; AAD42553.1; -; Genomic_DNA.
DR PIR; A00554; XYBPT4.
DR RefSeq; NP_049647.1; NC_000866.4.
DR PDB; 1Q0S; X-ray; 2.30 A; A=1-259.
DR PDB; 1Q0T; X-ray; 3.10 A; A/B=1-259.
DR PDB; 1YF3; X-ray; 2.29 A; A/B=1-259.
DR PDB; 1YFJ; X-ray; 2.69 A; A/B/C/D/E/F=1-259.
DR PDB; 1YFL; X-ray; 3.09 A; A/B/D/E=1-259.
DR PDBsum; 1Q0S; -.
DR PDBsum; 1Q0T; -.
DR PDBsum; 1YF3; -.
DR PDBsum; 1YFJ; -.
DR PDBsum; 1YFL; -.
DR SMR; P04392; -.
DR DrugBank; DB01752; S-adenosyl-L-homocysteine.
DR REBASE; 2837; M.EcoT4Dam.
DR PRIDE; P04392; -.
DR GeneID; 1258548; -.
DR KEGG; vg:1258548; -.
DR BRENDA; 2.1.1.72; 732.
DR EvolutionaryTrace; P04392; -.
DR Proteomes; UP000009087; Genome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009008; F:DNA-methyltransferase activity; IDA:CACAO.
DR GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IEA:UniProtKB-EC.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0099018; P:evasion by virus of host restriction-modification system; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IMP:CACAO.
DR Gene3D; 1.10.1020.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR023095; Ade_MeTrfase_dom_2.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR012263; M_m6A_EcoRV.
DR InterPro; IPR012327; MeTrfase_D12.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR30481; PTHR30481; 1.
DR Pfam; PF02086; MethyltransfD12; 1.
DR PIRSF; PIRSF000398; M_m6A_EcoRV; 1.
DR PRINTS; PR00505; D12N6MTFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00571; dam; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-binding; Host-virus interaction;
KW Methyltransferase; Reference proteome;
KW Restriction-modification system evasion by virus; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..259
FT /note="DNA adenine methylase"
FT /id="PRO_0000087990"
FT BINDING 7
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1Q0T,
FT ECO:0007744|PDB:1YF3, ECO:0007744|PDB:1YFJ"
FT BINDING 11
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1YF3,
FT ECO:0007744|PDB:1YFJ"
FT BINDING 32..37
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1Q0T,
FT ECO:0007744|PDB:1YF3, ECO:0007744|PDB:1YFJ"
FT BINDING 50
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1Q0T,
FT ECO:0007744|PDB:1YF3, ECO:0007744|PDB:1YFJ"
FT BINDING 156..157
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1YF3,
FT ECO:0007744|PDB:1YFJ"
FT BINDING 171
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1YF3,
FT ECO:0007744|PDB:1YFJ"
FT BINDING 181
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0007744|PDB:1Q0S, ECO:0007744|PDB:1Q0T,
FT ECO:0007744|PDB:1YF3, ECO:0007744|PDB:1YFJ"
FT MUTAGEN 126
FT /note="P->A,C,G: Hypermethylates DNA."
FT /evidence="ECO:0000269|PubMed:2510127"
FT MUTAGEN 126
FT /note="P->E,F,H: Loss of methylase activity."
FT /evidence="ECO:0000269|PubMed:2510127"
FT MUTAGEN 126
FT /note="P->S: In damh; hypermethylating mutant."
FT /evidence="ECO:0000269|PubMed:2510127"
FT MUTAGEN 127
FT /note="F->V: No longer methylates hmC-DNA-containing DNA."
FT /evidence="ECO:0000269|PubMed:2510127"
FT CONFLICT 139..140
FT /note="QY -> RF (in Ref. 2; X17641)"
FT /evidence="ECO:0000305"
FT CONFLICT 209
FT /note="Q -> L (in Ref. 2; X17641)"
FT /evidence="ECO:0000305"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 15..20
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 67..76
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 84..97
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 100..107
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 136..146
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 147..149
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 150..153
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 166..170
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:1YFL"
FT HELIX 180..184
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 187..201
FT /evidence="ECO:0007829|PDB:1YF3"
FT TURN 202..204
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 206..215
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 221..227
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 230..234
FT /evidence="ECO:0007829|PDB:1YF3"
FT HELIX 237..242
FT /evidence="ECO:0007829|PDB:1YF3"
FT STRAND 254..258
FT /evidence="ECO:0007829|PDB:1YF3"
SQ 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
