>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473 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 R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.

Probab=99.53  E-value=1.5e-13  Score=100.40  Aligned_cols=161  Identities=18%  Similarity=0.252  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHH----------CC-CEEEEECCCCCHHHHHHHHHHHHH--H-CCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf             89999999996----------79-809995889986899999999999--7-5999499991604656999999998558
Q gi|255764515|r    6 HQTKIVDWILD----------HK-RCAIWASMGSGKTVSVLTALSYIH--L-WGEKSVLVIAPLRVAQSVWTSEVQRWSN   71 (458)
Q Consensus         6 ~Q~~~v~~~~~----------~~-~~ll~~~~G~GKT~~al~~~~~l~--~-~~~~~~LIv~P~~l~~~~W~~Ei~kf~~   71 (458)
T Consensus       301 ~qy~av~ki~~~~~~~~~~k~~~n~G~iWHtQGSGKtlTm~f~A~k~~~~~~~~~p~v~fvvDR~eLd~Ql~~~~~~~~~  380 (813)
T TIGR00348       301 MQYRAVKKIVESILRKEKGKDKRNKGLIWHTQGSGKTLTMLFLARKLRKQKELKNPKVFFVVDRRELDEQLYKEFSSLKD  380 (813)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHHH
T ss_conf             99999999999998531378863674489850763788999999999874652698499997272778899999987642


Q ss_pred             CCCCEEEEEECCHHHHHH-HHCCC----------CCEEEECCCCHHH----HHHHCCCCCCCC--------EEECCCCCC
Q ss_conf             888159998589789888-73077----------9869980642023----344200011322--------044045310
Q gi|255764515|r   72 FSHMNISVITGTVKQRTK-VLKTP----------AVLYVINFENLGW----LVQELKGTWPFA--------TIVVDESTK  128 (458)
Q Consensus        72 ~~~~~~~~~~g~~~~r~~-~~~~~----------~~i~i~s~e~~~~----~~~~~~~~~~~~--------~iIiDEaH~  128 (458)
T Consensus       381 -~~~~~~~~~eS~~~Lk~~L~~~~~sennPn~~k~g~~~t~IqKF~~~~~~k~~e~~~~~~~~i~~~r~~vv~i~DEaHR  459 (813)
T TIGR00348       381 -LIKDCAERIESIAELKELLEKNDESENNPNISKRGIIITTIQKFDDELLDKLKEEEEKFPESIIIDRKEVVVIIDEAHR  459 (813)
T ss_pred             -HCHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCC
T ss_conf             -0101042067888999987517764567553567679996001040344536888743873689871608999706755


Q ss_pred             CCCCC------CCCHHHHHHHHHHHHHCCCEEEEECCCCHHHHCCC
Q ss_conf             02465------43115677776654305980799658402310010
Q gi|255764515|r  129 LKSFR------LRQGSKTARALAKPAWESERFIELTGTPSPNGLID  168 (458)
Q Consensus       129 lkn~~------~~~~s~~~~~l~~~~~~~~~~l~LTgTPi~n~~~e  168 (458)
T Consensus       460 sqyG~tqklhnGkfqtGla~~~~~~lknA-~f~gFTGTPI~~~d~~  504 (813)
T TIGR00348       460 SQYGKTQKLHNGKFQTGLAKALKKALKNA-SFFGFTGTPISKKDRD  504 (813)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCHHH-HHHCCCCCCCCHHCCC
T ss_conf             53534110004413589999998743112-0101224776532477