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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
 
 
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