>TIGR00497 hsdM type I restriction-modification system, M subunit; InterPro: IPR004546 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the M subunit (HsdM) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC. The M subunit (HsdM) functions in methylation of specific adenine residues, which is required for both restriction and modification activities , , . Methylation of specific residues prevents the host from digesting its own genome via its restriction enzymes. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence: when the target site is unmodified, the DNA is cut; when the target site is hemi-methylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0006306 DNA methylation.

Probab=100.00 E-value=0 Score=347.05 Aligned_cols=424 Identities=25% Similarity=0.448 Sum_probs=299.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCEEEHHHHHHHHHHHCCHHHHHHH-HHHHHCCCCCCCHHHHHH--------HCCC Q ss_conf 8889999999998740688834308723054899989674123399999-999720246889678765--------3389 Q gi|254780836|r 8 AASLANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVR-EKYLAFGGSNIDLESFVK--------VAGY 78 (674) Q Consensus 8 ~s~L~s~iW~~Ad~LRg~~~~~eY~~~ILp~~~Lrrld~~le~~k~~v~-~~~~~~~~~~~~~~~~~~--------~~g~ 78 (674) T Consensus 2 ~~~~~~~~w~~~~~~~g~~dgwd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 81 (516) T TIGR00497 2 RNELEKKIWEIANDLRGSVDGWDFKQYVLGGLFYRFLSENLANYINDGERKNDPSFDYAKLPDDYIEKLPLGRKALLFTK 81 (516) T ss_pred CCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHH T ss_conf 42045688876665313335420367899999999886667765300210256554212133577776533344555442 Q ss_pred CCC-CCCCCCHHHH---HH----HHHHHHHHHHHH----------H-HCHHHHHHHHHCCHHHHHHHH-----HHCCHHH Q ss_conf 610-3680368861---34----558999999997----------5-299989998717723577544-----4236289 Q gi|254780836|r 79 SFY-NTSEYSLSTL---GS----TNTRNNLESYIA----------S-FSDNAKAIFEDFDFSSTIARL-----EKAGLLY 134 (674) Q Consensus 79 ~F~-n~s~~~~~~l---~~----~~~~~nl~~yi~----------g-fS~nv~dI~~~f~f~~~i~~L-----~~~~~L~ 134 (674) T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~g~~~~~~~~~g~~~d~~~~~~--~~g~~~~~~~~~~~ 159 (516) T TIGR00497 82 GFFLPPSRLFLNALKNACENKNNEDLNTTLRDIFDDIEKSTELGDGRSEENFKGLFKDLDVNEN--KLGSTLTNRTEKLK 159 (516) T ss_pred HHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHH--HCCCHHHHHHHHHH T ss_conf 1000068999999988751356311355688877665422014776421334334420342111--11411345688899 Q ss_pred HHHHHHCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCHHCCCCCCCCEEECCCC Q ss_conf 9998740245673337-611443899999999986227665753681799999999731784011013877640311766 Q gi|254780836|r 135 KICKNFSGIELHPDTV-PDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPT 213 (674) Q Consensus 135 ~vI~~F~~idL~p~~v-~n~~mG~iyE~LIrkFae~~~~~aGeffTPR~Vi~Lmv~ll~~~~~~~~~~~p~~~~tIyDPa 213 (674) T Consensus 160 ~~~~~~~~~~~~~~~~~~~d~~gd~~~~~~~~~~~~~g~~gg~~~~p~~~~~~~~~~~~~~~~~--------~~~~~d~~ 231 (516) T TIGR00497 160 ELLEAIGGLELGDFLKNGIDAFGDAYEFLLALYASNAGKSGGEFFTPQDVSELLAKIALGGKDT--------VDDVYDPC 231 (516) T ss_pred HHHHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCH--------HHHHHHHC T ss_conf 9987513300012433010010047899999875204656665446255898988764045200--------23444310 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC----- Q ss_conf 540468999999999853100533322550466667889999999898088753345666682347545799986----- Q gi|254780836|r 214 CGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSKNIQQGSTLSKDLFT----- 288 (674) Q Consensus 214 CGTGGmL~~a~~~i~~~~~~~~~~~~~~lyGQEin~~tyaIak~nMli~g~~~d~~~~~~~NI~~GdTL~~d~~~----- 288 (674) T Consensus 232 cg~g~~~~~~~~~~g---~~--~~~~~~~~g~~~~~~~~~~c~~~~~~~~~~~~-----~~~~~~~d~~~~~~~~~~~~~ 301 (516) T TIGR00497 232 CGSGSLLLQFSKVLG---KD--KNSLKGYFGQEINLTTYNLCRLNLFLHDIDYA-----NFNIANGDTLLDPEWEKHYVN 301 (516) T ss_pred CCCCHHHHHHHHHHC---CC--HHHHHHHCCCHHCCHHHHHHHHHHHHHHCCCC-----CCEECCCCCCCCCHHHHCCCC T ss_conf 475136778787732---31--01122220210011034455554555312300-----100002310036201210012 Q ss_pred ---CCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCC-C-CCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEC-CC Q ss_conf ---64189998168567653100011123442266665357-7-774770659999999996146657880799973-89 Q gi|254780836|r 289 ---GKRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGP-G-LPKISDGSMLFLMHLANKLELPPNGGGRAAIVL-SS 362 (674) Q Consensus 289 ---~~kFD~vlaNPPFg~~Wk~~~~~v~~e~~~~~~~Rf~~-g-lP~~sdg~~lFlqh~i~klk~~~~~ggr~aIV~-ng 362 (674) T Consensus 302 c~~~~~~~~~~~~pp~~~~w~gd~~~~~~-----~d~~~~~~g~~~p~~~~d~~~~~~~~~~~~~~----g~~~~~~~pg 372 (516) T TIGR00497 302 CSDDEGFDAVVSNPPYSTKWAGDKNPNLV-----NDERFKPAGTLAPNNKADLAFTLHALYYLGNE----GTAAIVCFPG 372 (516) T ss_pred CCCCCCCEEEECCCCCCEEECCCCCCCEE-----CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC----CCEEEEECCC T ss_conf 46777732455378742000466544200-----10102533222655113588888898873256----6423222142 Q ss_pred CCCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEEECHHHHHHHHHCCCCCC Q ss_conf 71347764432689999998849468883176776557886169999946887434883899723677657640466442 Q gi|254780836|r 363 SPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKTEERRGKVQLINATDLWTSIRNEGKKRR 442 (674) Q Consensus 363 s~LF~G~agsGEs~IRk~lie~d~ieaII~LP~~lFynTgI~t~Iwil~k~K~~~rkgkV~lIDAs~~~~~~rk~G~Kr~ 442 (674) T Consensus 373 -~~~~~~~---~~~~~~~~~~~~~~d~~~~~p~~~~~~~~~~~~~~~~~~~~--~~~d~~~~~d~~~~~~~~----~~~~ 442 (516) T TIGR00497 373 -VLYRGGK---EAKIREYLVDENFVDCVIALPDNLFFGTSIATCILVLKKNK--DKDDPTLFIDGSNEFVKE----GKNN 442 (516) T ss_pred -HHCCCCC---HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC--CCCCCEEEEECCHHHHHC----CCCC T ss_conf -1103750---35688776420134555430100110124555443321256--755635786162344430----1012 Q ss_pred CCCHHHHHHHHHHHHHCCCCC-CEEEEEC Q ss_conf 069899999999997210254-1047444 Q gi|254780836|r 443 IINDDQRRQILDIYVSRENGK-FSRMLDY 470 (674) Q Consensus 443 ~l~~~~i~~Iv~~y~~f~e~e-~ski~~~ 470 (674) T Consensus 443 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 471 (516) T TIGR00497 443 KLKPKNREKILDCFNEKKEEKNFCKLAER 471 (516) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 34523678899877545566777776544

HHsearch alignment for GI: 254780836 and conserved domain: TIGR00497