MTH3_HAEAE
ID MTH3_HAEAE Reviewed; 330 AA.
AC P20589;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Type II methyltransferase M.HaeIII {ECO:0000303|PubMed:12654995};
DE Short=M.HaeIII {ECO:0000303|PubMed:1932026};
DE EC=2.1.1.37 {ECO:0000269|PubMed:1932026};
DE AltName: Full=Cytosine-specific methyltransferase HaeIII;
DE AltName: Full=Modification methylase HaeIII;
GN Name=haeIIIM;
OS Haemophilus aegyptius.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=197575;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 11116 / CCUG 25716 / NCTC 8502 / 180-a;
RX PubMed=3248732; DOI=10.1016/0378-1119(88)90248-x;
RA Slatko B.E., Croft R., Moran L.S., Wilson G.G.;
RT "Cloning and analysis of the HaeIII and HaeII methyltransferase genes.";
RL Gene 74:45-50(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 11116 / CCUG 25716 / NCTC 8502 / 180-a;
RA Zhang B.-H., Wilson G.G.;
RL Submitted (FEB-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROTEIN SEQUENCE OF 62-81, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, AND
RP DNA-BINDING.
RX PubMed=1932026; DOI=10.1021/bi00110a002;
RA Chen L., McMillan A.M., Chang W., Ezak-Nipkay K., Lane W.S., Verdine G.L.;
RT "Direct identification of the active-site nucleophile in a DNA (cytosine-
RT 5)-methyltransferase.";
RL Biochemistry 30:11018-11025(1991).
RN [4]
RP NOMENCLATURE.
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 [5] {ECO:0007744|PDB:1DCT}
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH DNA, AND SUBUNIT.
RX PubMed=7606780; DOI=10.1016/0092-8674(95)90060-8;
RA Reinisch K.M., Chen L., Verdine G.L., Lipscomb W.N.;
RT "The crystal structure of HaeIII methyltransferase covalently complexed to
RT DNA: an extrahelical cytosine and rearranged base pairing.";
RL Cell 82:143-153(1995).
RN [6] {ECO:0007744|PDB:3UBT}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF MUTANT SER-71 IN COMPLEX WITH
RP ATP, SUBUNIT, AND MUTAGENESIS OF CYS-71.
RX PubMed=23012373; DOI=10.1074/jbc.m112.413054;
RA Didovyk A., Verdine G.L.;
RT "Structural origins of DNA target selection and nucleobase extrusion by a
RT DNA cytosine methyltransferase.";
RL J. Biol. Chem. 287:40099-40105(2012).
CC -!- FUNCTION: A methylase, recognizes the double-stranded sequence 5'-GGCC-
CC 3', methylates C-3 on both strands, and protects the DNA from cleavage
CC by the HaeIII endonuclease. {ECO:0000269|PubMed:1932026,
CC ECO:0000303|PubMed:12654995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-
CC methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:13681, Rhea:RHEA-COMP:11369, Rhea:RHEA-COMP:11370,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:85452, ChEBI:CHEBI:85454; EC=2.1.1.37;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10018,
CC ECO:0000269|PubMed:1932026};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23012373,
CC ECO:0000269|PubMed:7606780}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
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DR EMBL; M24625; AAA24970.1; -; Genomic_DNA.
DR EMBL; AF051375; AAC05696.1; -; Genomic_DNA.
DR PIR; JS0102; JS0102.
DR RefSeq; WP_013527695.1; NZ_UGHG01000002.1.
DR PDB; 1DCT; X-ray; 2.80 A; A/B=1-324.
DR PDB; 3UBT; X-ray; 2.50 A; A/B/Y=1-330.
DR PDBsum; 1DCT; -.
DR PDBsum; 3UBT; -.
DR AlphaFoldDB; P20589; -.
DR SMR; P20589; -.
DR REBASE; 3410; M.HaeIII.
DR BRENDA; 2.1.1.37; 2525.
DR EvolutionaryTrace; P20589; -.
DR PRO; PR:P20589; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009307; P:DNA restriction-modification system; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018117; C5_DNA_meth_AS.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR031303; C5_meth_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS00094; C5_MTASE_1; 1.
DR PROSITE; PS00095; C5_MTASE_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Direct protein sequencing; DNA-binding;
KW Methyltransferase; Nucleotide-binding; Restriction system;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..330
FT /note="Type II methyltransferase M.HaeIII"
FT /id="PRO_0000087878"
FT DOMAIN 1..327
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT ACT_SITE 71
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018,
FT ECO:0000269|PubMed:1932026"
FT BINDING 29
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:3UBT"
FT BINDING 50..51
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:3UBT"
FT BINDING 260
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0007744|PDB:3UBT"
FT MUTAGEN 71
FT /note="C->S: No longer has methyltransferase activity,
FT binds DNA in a wild-type manner."
FT /evidence="ECO:0000269|PubMed:23012373"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 12..19
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 23..29
FT /evidence="ECO:0007829|PDB:3UBT"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 35..41
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:1DCT"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:1DCT"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 89..101
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 104..110
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 113..116
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:1DCT"
FT HELIX 121..133
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 135..143
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 154..162
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 186..188
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 242..244
FT /evidence="ECO:0007829|PDB:1DCT"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:3UBT"
FT STRAND 261..263
FT /evidence="ECO:0007829|PDB:3UBT"
FT TURN 266..268
FT /evidence="ECO:0007829|PDB:1DCT"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 277..284
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 297..305
FT /evidence="ECO:0007829|PDB:3UBT"
FT HELIX 310..326
FT /evidence="ECO:0007829|PDB:3UBT"
SQ SEQUENCE 330 AA; 37686 MW; 928C6D5390DBED25 CRC64;
MNLISLFSGA GGLDLGFQKA GFRIICANEY DKSIWKTYES NHSAKLIKGD ISKISSDEFP
KCDGIIGGPP CQSWSEGGSL RGIDDPRGKL FYEYIRILKQ KKPIFFLAEN VKGMMAQRHN
KAVQEFIQEF DNAGYDVHII LLNANDYGVA QDRKRVFYIG FRKELNINYL PPIPHLIKPT
FKDVIWDLKD NPIPALDKNK TNGNKCIYPN HEYFIGSYST IFMSRNRVRQ WNEPAFTVQA
SGRQCQLHPQ APVMLKVSKN LNKFVEGKEH LYRRLTVREC ARVQGFPDDF IFHYESLNDG
YKMIGNAVPV NLAYEIAKTI KSALEICKGN
