ID T1M_BACTN Reviewed; 472 AA.
AC Q89Z59;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 27-MAR-2024, entry version 123.
DE RecName: Full=Type I restriction enzyme BthVORF4518P methylase subunit;
DE Short=M protein;
DE EC=2.1.1.72 {ECO:0000250|UniProtKB:P08957};
DE AltName: Full=Type I methyltransferase M.BthVORF4518P {ECO:0000303|PubMed:12654995};
DE Short=M.BthVORF4518P;
GN Name=hsdM {ECO:0000305}; OrderedLocusNames=BT_4518;
OS Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 /
OS CCUG 10774 / NCTC 10582 / VPI-5482 / E50).
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=226186;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=12663928; DOI=10.1126/science.1080029;
RA Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C.,
RA Hooper L.V., Gordon J.I.;
RT "A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.";
RL Science 299:2074-2076(2003).
RN [2]
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 [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE.
RG Joint center for structural genomics (JCSG);
RT "Crystal structure of type I restriction enzyme protein (NP_813429.1) from
RT bacteriodes thetaiotaomicron VPI-5482 at 2.20 A resolution resolution.";
RL Submitted (JAN-2007) to the PDB data bank.
CC -!- FUNCTION: The subtype gamma methyltransferase (M) subunit of a type I
CC restriction enzyme. The M and S subunits together form a
CC methyltransferase (MTase) that methylates two adenine residues of an
CC undetermined sequence. In the presence of the R subunit the complex can
CC also act as an endonuclease, binding to the same target sequence but
CC cutting the DNA some distance from this site. Whether the DNA is cut or
CC modified depends on the methylation state of the target sequence. When
CC the target site is unmodified, the DNA is cut. When the target site is
CC hemimethylated, the complex acts as a maintenance MTase modifying the
CC DNA so that both strands become methylated. After locating a non-
CC methylated recognition site, the enzyme complex serves as a molecular
CC motor that translocates DNA in an ATP-dependent manner until a
CC collision occurs that triggers cleavage. {ECO:0000250|UniProtKB:P08957,
CC ECO:0000303|PubMed:12654995}.
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:0000250|UniProtKB:P08957};
CC -!- SUBUNIT: The type I restriction/modification system is composed of
CC three polypeptides R, M and S; the restriction enzyme has stoichiometry
CC R(2)M(2)S(1) while the methyltransferase is M(2)S(1).
CC {ECO:0000250|UniProtKB:P08957}.
CC -!- MISCELLANEOUS: Type I restriction and modification enzymes are complex,
CC multifunctional systems which require ATP, S-adenosyl methionine and
CC Mg(2+) as cofactors and, in addition to their endonucleolytic and
CC methylase activities, are potent DNA-dependent ATPases.
CC {ECO:0000250|UniProtKB:P08957}.
CC -!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
CC {ECO:0000305}.
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DR EMBL; AE015928; AAO79623.1; -; Genomic_DNA.
DR RefSeq; NP_813429.1; NC_004663.1.
DR RefSeq; WP_011109305.1; NC_004663.1.
DR PDB; 2OKC; X-ray; 2.20 A; A/B=1-444.
DR PDBsum; 2OKC; -.
DR AlphaFoldDB; Q89Z59; -.
DR SMR; Q89Z59; -.
DR STRING; 226186.BT_4518; -.
DR REBASE; 191896; M.Apa1447ORF2439P.
DR REBASE; 246644; M.Mmy2708ORF27P.
DR REBASE; 403240; Ssp8227ORF2875P.
DR REBASE; 7071; M.BthVORF4518P.
DR PaxDb; 226186-BT_4518; -.
DR DNASU; 1073274; -.
DR EnsemblBacteria; AAO79623; AAO79623; BT_4518.
DR GeneID; 60925694; -.
DR KEGG; bth:BT_4518; -.
DR PATRIC; fig|226186.12.peg.4602; -.
DR eggNOG; COG0286; Bacteria.
DR HOGENOM; CLU_018284_2_0_10; -.
DR InParanoid; Q89Z59; -.
DR OrthoDB; 9814572at2; -.
DR EvolutionaryTrace; Q89Z59; -.
DR PRO; PR:Q89Z59; -.
DR Proteomes; UP000001414; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008170; F:N-methyltransferase activity; IEA:InterPro.
DR GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IEA:UniProtKB-EC.
DR GO; GO:0009307; P:DNA restriction-modification system; IEA:UniProtKB-KW.
DR Gene3D; 1.20.1260.30; -; 1.
DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR InterPro; IPR022749; D12N6_MeTrfase_N.
DR InterPro; IPR003356; DNA_methylase_A-5.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR038333; T1MK-like_N_sf.
DR PANTHER; PTHR42933; SLR6095 PROTEIN; 1.
DR PANTHER; PTHR42933:SF4; TYPE I RESTRICTION ENZYME ECOKI METHYLASE SUBUNIT; 1.
DR Pfam; PF12161; HsdM_N; 1.
DR Pfam; PF02384; N6_Mtase; 1.
DR PRINTS; PR00507; N12N6MTFRASE.
DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Methyltransferase; Reference proteome;
KW Restriction system; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..472
FT /note="Type I restriction enzyme BthVORF4518P methylase
FT subunit"
FT /id="PRO_0000310988"
FT BINDING 151..156
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|Ref.3, ECO:0007744|PDB:2OKC"
FT BINDING 181..183
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|Ref.3, ECO:0007744|PDB:2OKC"
FT BINDING 214
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|Ref.3, ECO:0007744|PDB:2OKC"
FT BINDING 243..244
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|Ref.3, ECO:0007744|PDB:2OKC"
FT HELIX 11..24
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 29..51
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 64..68
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 73..87
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 91..96
FT /evidence="ECO:0007829|PDB:2OKC"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 107..118
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 128..142
FT /evidence="ECO:0007829|PDB:2OKC"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 183..193
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 200..207
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 210..215
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 217..229
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:2OKC"
FT TURN 244..246
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 284..295
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 296..307
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 308..312
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 316..327
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 328..335
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 338..343
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 348..357
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 360..366
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 375..378
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 382..385
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 386..393
FT /evidence="ECO:0007829|PDB:2OKC"
FT TURN 401..403
FT /evidence="ECO:0007829|PDB:2OKC"
FT STRAND 408..413
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 414..419
FT /evidence="ECO:0007829|PDB:2OKC"
FT HELIX 421..423
FT /evidence="ECO:0007829|PDB:2OKC"
SQ SEQUENCE 472 AA; 53127 MW; 3891797D2845329D CRC64;
MATNSSTEQS LTKKVWNLAT TLAGQGIGFT DYITQLTYLL FLKMDAENVE MFGEESAIPT
GYQWADLIAF DGLDLVKQYE ETLKLLSELD NLIGTIYTKA QNKIDKPVYL KKVITMIDEE
QWLIMDGDVK GAIYESILEK NGQDKKSGAG QYFTPRPLIQ AMVDCINPQM GETVCDPACG
TGGFLLTAYD YMKGQSASKE KRDFLRDKAL HGVDNTPLVV TLASMNLYLH GIGTDRSPIV
CEDSLEKEPS TLVDVILANP PFGTRPAGSV DINRPDFYVE TKNNQLNFLQ HMMLMLKTGG
RAAVVLPDNV LFEAGAGETI RKRLLQDFNL HTILRLPTGI FYAQGVKANV LFFSKGQPTK
EIWFYDYRTD IKHTLATNKL ERHHLDDFVS CYNNRVEIYD AENNPQGRWR KYPVDEIIAR
DKTSLDITWI KPGGEVDDRS LAELMADIKD KSQTISRAVT ELEKLLANIE EN
//
