T1MK_ECOLI
ID T1MK_ECOLI Reviewed; 529 AA.
AC P08957; Q2M5W7;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1988, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Type I restriction enzyme EcoKI methylase subunit {ECO:0000305};
DE Short=M protein;
DE EC=2.1.1.72 {ECO:0000269|PubMed:8514761};
DE AltName: Full=Type I methyltransferase M.EcoKI {ECO:0000303|PubMed:12654995};
DE Short=M.EcoKI {ECO:0000303|PubMed:12654995};
GN Name=hsdM {ECO:0000303|PubMed:6255295}; Synonyms=hsm;
GN OrderedLocusNames=b4349, JW4312;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3323532; DOI=10.1016/0022-2836(87)90303-2;
RA Loenen W.A.M., Daniel A.S., Braymer H.D., Murray N.E.;
RT "Organization and sequence of the hsd genes of Escherichia coli K-12.";
RL J. Mol. Biol. 198:159-170(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 1-5, FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=8514761; DOI=10.1016/s0021-9258(19)38641-7;
RA Dryden D.T., Cooper L.P., Murray N.E.;
RT "Purification and characterization of the methyltransferase from the type 1
RT restriction and modification system of Escherichia coli K12.";
RL J. Biol. Chem. 268:13228-13236(1993).
RN [6]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=4868368; DOI=10.1038/2171110a0;
RA Meselson M., Yuan R.;
RT "DNA restriction enzyme from E. coli.";
RL Nature 217:1110-1114(1968).
RN [7]
RP FUNCTION, SUBUNIT, AND OPERON STRUCTURE.
RC STRAIN=K12;
RX PubMed=6255295; DOI=10.1007/bf00267350;
RA Sain B., Murray N.E.;
RT "The hsd (host specificity) genes of E. coli K 12.";
RL Mol. Gen. Genet. 180:35-46(1980).
RN [8]
RP FUNCTION, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=9033396; DOI=10.1021/bi9619435;
RA Dryden D.T., Cooper L.P., Thorpe P.H., Byron O.;
RT "The in vitro assembly of the EcoKI type I DNA restriction/modification
RT enzyme and its in vivo implications.";
RL Biochemistry 36:1065-1076(1997).
RN [9]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [10]
RP INTERACTION WITH ESCHERICHIA PHAGE T7 PROTEIN OCR (MICROBIAL INFECTION).
RC STRAIN=K12;
RX PubMed=12235377; DOI=10.1093/nar/gkf518;
RA Atanasiu C., Su T.J., Sturrock S.S., Dryden D.T.;
RT "Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI
RT restriction/modification enzyme.";
RL Nucleic Acids Res. 30:3936-3944(2002).
RN [11]
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 [12] {ECO:0007744|PDB:2AR0}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 2-527.
RA Rajashankar K.R., Kniewel R., Lima C.D.;
RT "Crystal structure of Type I restriction enzyme EcoKI M protein (EC
RT 2.1.1.72) (M.EcoKI).";
RL Submitted (AUG-2005) to the PDB data bank.
RN [13] {ECO:0007744|PDB:2Y7C, ECO:0007744|PDB:2Y7H}
RP STRUCTURE BY ELECTRON MICROSCOPY (18.00 ANGSTROMS) IN COMPLEX WITH
RP SPECIFICITY SUBUNIT AND ESCHERICHIA PHAGE T7 PROTEIN OCR, AND INTERACTION
RP WITH ESCHERICHIA PHAGE T7 PROTEIN OCR (MICROBIAL INFECTION).
RX PubMed=19074193; DOI=10.1093/nar/gkn988;
RA Kennaway C.K., Obarska-Kosinska A., White J.H., Tuszynska I., Cooper L.P.,
RA Bujnicki J.M., Trinick J., Dryden D.T.;
RT "The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic
RT antirestriction protein.";
RL Nucleic Acids Res. 37:762-770(2009).
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 A-2 on the top and A-3 on the
CC bottom strand of the sequence 5'-AACN(6)GTGC-3'. In the presence of the
CC R subunit the complex can also act as an endonuclease, binding to the
CC same target sequence but cutting the DNA some distance from this site.
CC Whether the DNA is cut or modified depends on the methylation state of
CC the target sequence. When the target site is unmodified, the DNA is
CC cut. When the target site is hemimethylated, the complex acts as a
CC maintenance MTase modifying the DNA so that both strands become
CC methylated. After locating a non-methylated recognition site, the
CC enzyme complex serves as a molecular motor that translocates DNA in an
CC ATP-dependent manner until a collision occurs that triggers cleavage.
CC {ECO:0000269|PubMed:4868368, ECO:0000269|PubMed:6255295,
CC ECO:0000269|PubMed:8514761, ECO:0000269|PubMed:9033396}.
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:8514761};
CC -!- SUBUNIT: The type I restriction/modification system is composed of
CC three polypeptides R, M and S (PubMed:6255295). The restriction enzyme
CC has stoichiometry R(2)M(2)S(1) (PubMed:9033396). The methyltransferase
CC is composed of M(2)S(1) (PubMed:8514761, PubMed:9033396,
CC PubMed:19074193). {ECO:0000269|PubMed:19074193,
CC ECO:0000269|PubMed:6255295, ECO:0000269|PubMed:8514761,
CC ECO:0000269|PubMed:9033396}.
CC -!- SUBUNIT: (Microbial infection) Interacts with Escherichia phage T7
CC protein Ocr; this interaction leads to the inhibition of the
CC methyltransferase restriction enzyme M.EcoKI composed of M(2)S(1).
CC {ECO:0000269|PubMed:12235377, ECO:0000269|PubMed:19074193}.
CC -!- INTERACTION:
CC P08957; P12295: ung; NbExp=3; IntAct=EBI-878571, EBI-559403;
CC -!- INDUCTION: Encoded in the hsd locus, in the order hsdR-hsdM-hsdS. There
CC is a promoter upstream of hsdR and another between hsdR and hsdM
CC (PubMed:6255295). This probably allows expression of the methylase
CC enzyme before the restriction-specific subunit (Probable).
CC {ECO:0000269|PubMed:6255295, ECO:0000305|PubMed:6255295}.
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 -!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
CC {ECO:0000305}.
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DR EMBL; X06545; CAA29792.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97246.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77305.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78339.1; -; Genomic_DNA.
DR PIR; B30375; XYECHM.
DR RefSeq; NP_418769.1; NC_000913.3.
DR RefSeq; WP_001063204.1; NZ_LN832404.1.
DR PDB; 2AR0; X-ray; 2.80 A; A/B=2-527.
DR PDB; 2Y7C; EM; 18.00 A; B/C=1-529.
DR PDB; 2Y7H; EM; 18.00 A; B/C=1-529.
DR PDBsum; 2AR0; -.
DR PDBsum; 2Y7C; -.
DR PDBsum; 2Y7H; -.
DR AlphaFoldDB; P08957; -.
DR SMR; P08957; -.
DR BioGRID; 4262768; 110.
DR ComplexPortal; CPX-5628; Type I restriction-modification EcoKI complex.
DR DIP; DIP-9943N; -.
DR IntAct; P08957; 15.
DR STRING; 511145.b4349; -.
DR REBASE; 13379; M.EcoW3110ORF4339P.
DR REBASE; 152630; M1.Ret561ORF1035P.
DR REBASE; 152641; M.Rsp1341ORF1035P.
DR REBASE; 152653; M.Rsp113ORF1037P.
DR REBASE; 152691; M.Rph931ORF1047P.
DR REBASE; 152704; M.Rph831ORF1044P.
DR REBASE; 152714; M.Rsp741ORF1035P.
DR REBASE; 152736; M.Rsp871ORF1035P.
DR REBASE; 156146; M.BamRD77ORF2498P.
DR REBASE; 204159; M.Bli1441ORF2992P.
DR REBASE; 204719; M.Bsu333ORF2986P.
DR REBASE; 205029; M.Bve72ORF2738P.
DR REBASE; 205122; M.Bve1413ORF3003P.
DR REBASE; 3387; M.EcoKI.
DR REBASE; 441884; M.EcoBL21FORF4361P.
DR jPOST; P08957; -.
DR PaxDb; P08957; -.
DR PRIDE; P08957; -.
DR EnsemblBacteria; AAC77305; AAC77305; b4349.
DR EnsemblBacteria; BAE78339; BAE78339; BAE78339.
DR GeneID; 948872; -.
DR KEGG; ecj:JW4312; -.
DR KEGG; eco:b4349; -.
DR PATRIC; fig|1411691.4.peg.2337; -.
DR EchoBASE; EB0453; -.
DR eggNOG; COG0286; Bacteria.
DR HOGENOM; CLU_018284_2_0_6; -.
DR InParanoid; P08957; -.
DR OMA; THRLALM; -.
DR PhylomeDB; P08957; -.
DR BioCyc; EcoCyc:EG10458-MON; -.
DR BioCyc; MetaCyc:EG10458-MON; -.
DR BRENDA; 3.1.21.3; 2165.
DR EvolutionaryTrace; P08957; -.
DR PRO; PR:P08957; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0019812; C:type I site-specific deoxyribonuclease complex; IPI:ComplexPortal.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008170; F:N-methyltransferase activity; IMP:EcoliWiki.
DR GO; GO:0009007; F:site-specific DNA-methyltransferase (adenine-specific) activity; IEA:UniProtKB-EC.
DR GO; GO:0009307; P:DNA restriction-modification system; IDA:ComplexPortal.
DR Gene3D; 1.20.1260.30; -; 1.
DR Gene3D; 3.40.50.150; -; 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 Pfam; PF12161; HsdM_N; 1.
DR Pfam; PF02384; N6_Mtase; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding;
KW Host-virus interaction; Methyltransferase; Reference proteome;
KW Restriction system; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..529
FT /note="Type I restriction enzyme EcoKI methylase subunit"
FT /id="PRO_0000088022"
FT BINDING 148..153
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q89Z59"
FT BINDING 178..180
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q89Z59"
FT BINDING 216
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q89Z59"
FT HELIX 5..18
FT /evidence="ECO:0007829|PDB:2AR0"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 27..43
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 46..49
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 56..60
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 64..78
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 84..90
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 153..163
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:2AR0"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:2AR0"
FT TURN 191..198
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 201..209
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 211..217
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 219..230
FT /evidence="ECO:0007829|PDB:2AR0"
FT TURN 231..233
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 242..247
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 260..265
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 288..299
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 300..311
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 312..316
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 320..331
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 332..339
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 352..360
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 374..379
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 388..391
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 395..397
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 399..405
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 427..429
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 433..435
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 442..444
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 446..451
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 452..457
FT /evidence="ECO:0007829|PDB:2AR0"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 482..505
FT /evidence="ECO:0007829|PDB:2AR0"
FT HELIX 511..521
FT /evidence="ECO:0007829|PDB:2AR0"
SQ SEQUENCE 529 AA; 59307 MW; D41C02203747C965 CRC64;
MNNNDLVAKL WKLCDNLRDG GVSYQNYVNE LASLLFLKMC KETGQEAEYL PEGYRWDDLK
SRIGQEQLQF YRKMLVHLGE DDKKLVQAVF HNVSTTITEP KQITALVSNM DSLDWYNGAH
GKSRDDFGDM YEGLLQKNAN ETKSGAGQYF TPRPLIKTII HLLKPQPREV VQDPAAGTAG
FLIEADRYVK SQTNDLDDLD GDTQDFQIHR AFIGLELVPG TRRLALMNCL LHDIEGNLDH
GGAIRLGNTL GSDGENLPKA HIVATNPPFG SAAGTNITRT FVHPTSNKQL CFMQHIIETL
HPGGRAAVVV PDNVLFEGGK GTDIRRDLMD KCHLHTILRL PTGIFYAQGV KTNVLFFTKG
TVANPNQDKN CTDDVWVYDL RTNMPSFGKR TPFTDEHLQP FERVYGEDPH GLSPRTEGEW
SFNAEETEVA DSEENKNTDQ HLATSRWRKF SREWIRTAKS DSLDISWLKD KDSIDADSLP
EPDVLAAEAM GELVQALSEL DALMRELGAS DEADLQRQLL EEAFGGVKE
