CCRM_CAUVC
ID CCRM_CAUVC Reviewed; 358 AA.
AC P0CAW2; Q45971;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 1.
DT 03-AUG-2022, entry version 64.
DE RecName: Full=DNA methyltransferase CcrM {ECO:0000250|UniProtKB:B8GZ33};
DE Short=M.CcrMI {ECO:0000303|PubMed:12654995};
DE EC=2.1.1.72;
DE AltName: Full=DNA adenine methyltransferase CcrM {ECO:0000303|PubMed:31601797};
DE AltName: Full=Type II methyltransferase M.CcrMI {ECO:0000303|PubMed:12654995};
GN Name=ccrMIM; Synonyms=ccrM {ECO:0000303|PubMed:31601797};
GN OrderedLocusNames=CC_0378;
OS Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Caulobacter.
OX NCBI_TaxID=190650;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=11259647; DOI=10.1073/pnas.061029298;
RA Nierman W.C., Feldblyum T.V., Laub M.T., Paulsen I.T., Nelson K.E.,
RA Eisen J.A., Heidelberg J.F., Alley M.R.K., Ohta N., Maddock J.R.,
RA Potocka I., Nelson W.C., Newton A., Stephens C., Phadke N.D., Ely B.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Gwinn M.L., Haft D.H., Kolonay J.F.,
RA Smit J., Craven M.B., Khouri H.M., Shetty J., Berry K.J., Utterback T.R.,
RA Tran K., Wolf A.M., Vamathevan J.J., Ermolaeva M.D., White O.,
RA Salzberg S.L., Venter J.C., Shapiro L., Fraser C.M.;
RT "Complete genome sequence of Caulobacter crescentus.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4136-4141(2001).
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] {ECO:0007744|PDB:6PBD}
RP X-RAY CRYSTALLOGRAPHY (2.34 ANGSTROMS) IN COMPLEX WITH DNA, FUNCTION,
RP REACTION MECHANISM, SUBUNIT, DOMAIN, AND DNA-BINDING.
RC STRAIN=ATCC 19089 / CB15;
RX PubMed=31601797; DOI=10.1038/s41467-019-12498-7;
RA Horton J.R., Woodcock C.B., Opot S.B., Reich N.O., Zhang X., Cheng X.;
RT "The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble
RT at its DNA recognition site.";
RL Nat. Commun. 10:4600-4600(2019).
CC -!- FUNCTION: A beta subtype methylase that recognizes the double-stranded
CC sequence 5'-GANTC-3' and methylates non-modifed A-2 on the
CC hemimethylated, post-replicative DNA (Probable) (PubMed:12654995) (By
CC similarity). Opens a bubble in the DNA at the recognition site,
CC allowing precise recognition of the sequence and ensuring enzyme
CC specificity (PubMed:31601797). Functions only in the predivisional
CC cell. Responsible for 5'-GANTC-3' methylation in the cell; methylation
CC of hemimethylated sites generated after replication fork passage occurs
CC late in the predivisional cell, near completion of chromosome
CC replication but prior to cell division. Contributes to the accurate
CC cell-cycle control of DNA replication and cellular morphology (By
CC similarity). {ECO:0000250|UniProtKB:B8GZ33,
CC ECO:0000269|PubMed:31601797, ECO:0000303|PubMed:12654995,
CC ECO:0000305|PubMed:31601797}.
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 -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:31601797}.
CC -!- DEVELOPMENTAL STAGE: Only expressed in predivisional cells, protein
CC levels drop precipitously prior to cell division.
CC {ECO:0000250|UniProtKB:B8GZ33}.
CC -!- INDUCTION: Transcribed from 80 minutes in synchronized cells.
CC {ECO:0000250|UniProtKB:B8GZ33}.
CC -!- DOMAIN: Has an N-terminal methyltransferase (MTase) domain linked to a
CC C-terminal DNA-binding domain by a 10 residue linker. The MTase of one
CC monomer recognizes, binds and modifies the target strand while C-
CC terminal domain of the other monomer binds the non-target strand.
CC {ECO:0000269|PubMed:31601797}.
CC -!- PTM: Rapidly degraded by Lon protease prior to cell division.
CC {ECO:0000250|UniProtKB:B8GZ33}.
CC -!- SIMILARITY: Belongs to the N(4)/N(6)-methyltransferase family.
CC {ECO:0000305}.
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DR EMBL; AE005673; AAK22365.1; -; Genomic_DNA.
DR PIR; A87296; A87296.
DR RefSeq; NP_419197.1; NC_002696.2.
DR RefSeq; WP_010918266.1; NC_002696.2.
DR PDB; 6PBD; X-ray; 2.34 A; A/B=1-358.
DR PDBsum; 6PBD; -.
DR AlphaFoldDB; P0CAW2; -.
DR SMR; P0CAW2; -.
DR STRING; 190650.CC_0378; -.
DR REBASE; 2539; M.CcrMI.
DR EnsemblBacteria; AAK22365; AAK22365; CC_0378.
DR KEGG; ccr:CC_0378; -.
DR PATRIC; fig|190650.5.peg.380; -.
DR eggNOG; COG2189; Bacteria.
DR HOGENOM; CLU_024927_5_1_5; -.
DR OMA; WRKANPM; -.
DR BioCyc; CAULO:CC0378-MON; -.
DR BRENDA; 2.1.1.72; 1218.
DR Proteomes; UP000001816; 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:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR002941; DNA_methylase_N4/N6.
DR InterPro; IPR002052; DNA_methylase_N6_adenine_CS.
DR InterPro; IPR040843; RAMA.
DR InterPro; IPR001091; RM_Methyltransferase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF01555; N6_N4_Mtase; 1.
DR Pfam; PF18755; RAMA; 1.
DR PRINTS; PR00508; S21N4MTFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-binding; Methyltransferase;
KW Reference proteome; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..358
FT /note="DNA methyltransferase CcrM"
FT /id="PRO_0000087987"
FT DOMAIN 259..355
FT /note="RAMA"
FT /evidence="ECO:0000255"
FT DNA_BIND 31..34
FT /note="Target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 39..45
FT /note="Target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 93..94
FT /note="Non-target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 109..110
FT /note="Non-target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 122..132
FT /note="Target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 153..157
FT /note="Non-target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 187..193
FT /note="Target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 315..317
FT /note="Non-target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT DNA_BIND 330..332
FT /note="Non-target strand DNA"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT REGION 1..260
FT /note="Methyltransferase"
FT /evidence="ECO:0000305|PubMed:31601797"
FT REGION 261..270
FT /note="Linker"
FT /evidence="ECO:0000305|PubMed:31601797"
FT REGION 272..358
FT /note="Non-specific DNA-binding"
FT /evidence="ECO:0000305|PubMed:31601797"
FT BINDING 94
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT BINDING 164
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT BINDING 179
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT BINDING 267
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT BINDING 272
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT BINDING 350
FT /ligand="dsDNA"
FT /ligand_id="ChEBI:CHEBI:4705"
FT /evidence="ECO:0000269|PubMed:31601797,
FT ECO:0007744|PDB:6PBD"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 13..19
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 25..30
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 63..80
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 81..91
FT /evidence="ECO:0007829|PDB:6PBD"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 96..105
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 109..120
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 134..142
FT /evidence="ECO:0007829|PDB:6PBD"
FT TURN 153..157
FT /evidence="ECO:0007829|PDB:6PBD"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 176..178
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 195..205
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 211..216
FT /evidence="ECO:0007829|PDB:6PBD"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 221..228
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 240..251
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 275..280
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 293..296
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 307..309
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 316..322
FT /evidence="ECO:0007829|PDB:6PBD"
FT TURN 323..325
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 331..334
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:6PBD"
FT STRAND 340..345
FT /evidence="ECO:0007829|PDB:6PBD"
FT HELIX 347..356
FT /evidence="ECO:0007829|PDB:6PBD"
SQ SEQUENCE 358 AA; 39665 MW; 05F43266F7D4C614 CRC64;
MKFGPETIIH GDCIEQMNAL PEKSVDLIFA DPPYNLQLGG DLLRPDNSKV DAVDDHWDQF
ESFAAYDKFT REWLKAARRV LKDDGAIWVI GSYHNIFRVG VAVQDLGFWI LNDIVWRKSN
PMPNFKGTRF ANAHETLIWA SKSQNAKRYT FNYDALKMAN DEVQMRSDWT IPLCTGEERI
KGADGQKAHP TQKPEALLYR VILSTTKPGD VILDPFFGVG TTGAAAKRLG RKFIGIEREA
EYLEHAKARI AKVVPIAPED LDVMGSKRAE PRVPFGTIVE AGLLSPGDTL YCSKGTHVAK
VRPDGSITVG DLSGSIHKIG ALVQSAPACN GWTYWHFKTD AGLAPIDVLR AQVRAGMN
