T1RK_ECOLI
ID T1RK_ECOLI Reviewed; 1170 AA.
AC P08956; Q2M5W6;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 3.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=Type I restriction enzyme EcoKI endonuclease subunit {ECO:0000303|PubMed:12654995};
DE Short=EcoKI {ECO:0000303|PubMed:12654995};
DE Short=R protein;
DE EC=3.1.21.3 {ECO:0000269|PubMed:4868368};
GN Name=hsdR {ECO:0000303|PubMed:6255295}; Synonyms=hsr;
GN OrderedLocusNames=b4350, JW4313;
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-9.
RC STRAIN=K12 / CR63;
RX PubMed=1650347; DOI=10.1128/jb.173.16.5207-5219.1991;
RA Waite-Rees P.A., Keating C.J., Moran L.S., Slatko B.E., Hornstra L.J.,
RA Benner J.S.;
RT "Characterization and expression of the Escherichia coli Mrr restriction
RT system.";
RL J. Bacteriol. 173:5207-5219(1991).
RN [6]
RP PROTEIN SEQUENCE OF 1-6 AND 2-6, 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 [7]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ATP AND
RP S-ADENOSYL-METHIONINE REQUIREMENT, AND BIOPHYSICOCHEMICAL PROPERTIES.
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 [8]
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 [9]
RP FUNCTION, AND REACTION MECHANISM.
RC STRAIN=K12;
RX PubMed=6248234; DOI=10.1016/0092-8674(80)90251-2;
RA Yuan R., Hamilton D.L., Burckhardt J.;
RT "DNA translocation by the restriction enzyme from E. coli K.";
RL Cell 20:237-244(1980).
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]
RP SUBUNIT, INTERACTION WITH ESCHERICHIA PHAGE T7 PROTEIN OCR (MICROBIAL
RP INFECTION), AND DOMAIN.
RX PubMed=32483229; DOI=10.1038/s41564-020-0731-z;
RA Gao Y., Cao D., Zhu J., Feng H., Luo X., Liu S., Yan X.X., Zhang X.,
RA Gao P.;
RT "Structural insights into assembly, operation and inhibition of a type I
RT restriction-modification system.";
RL Nat. Microbiol. 5:1107-1118(2020).
CC -!- FUNCTION: The subtype A restriction (R) subunit of a type I restriction
CC enzyme that recognizes 5'-AACN(6)GTGC-3' and cleaves a random distance
CC away. The R subunit is required for both endonuclease and ATPase
CC activities but not for modification (PubMed:4868368, PubMed:6255295,
CC PubMed:12654995, PubMed:9033396). Has endonucleolytic activity that
CC requires Mg(2+), ATP and S-adenosyl-L-methionine (SAM); ATP can be
CC replaced by dATP, no tested molecule could substitute for SAM.
CC Generates double-stranded DNA with no nicks, by cutting one strand then
CC the other within a few seconds. Cleaves only non-methylated DNA, hemi-
CC methylated and fully methylated DNA are not substrates (PubMed:4868368,
CC PubMed:9033396). 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 (PubMed:6248234). {ECO:0000269|PubMed:4868368,
CC ECO:0000269|PubMed:6248234, ECO:0000269|PubMed:6255295,
CC ECO:0000269|PubMed:9033396, ECO:0000303|PubMed:12654995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of DNA to give random double-stranded
CC fragments with terminal 5'-phosphates, ATP is simultaneously
CC hydrolyzed.; EC=3.1.21.3; Evidence={ECO:0000269|PubMed:4868368};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5-8.0 for DNA restriction.
CC {ECO:0000269|PubMed:4868368};
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, PubMed:32483229). The
CC methyltransferase is composed of M(2)S(1) (PubMed:9033396) (Probable).
CC {ECO:0000269|PubMed:32483229, ECO:0000269|PubMed:6255295,
CC ECO:0000269|PubMed:9033396, ECO:0000305|PubMed:32483229}.
CC -!- SUBUNIT: (Microbial infection) Interacts with Escherichia phage T7
CC protein Ocr; this interaction leads to the inhibition of the type I
CC bifunctional endonuclease and methyltransferase restriction enzyme
CC R.EcoKI composed of R(2)M(2)S(1). {ECO:0000269|PubMed:12235377,
CC ECO:0000269|PubMed:32483229}.
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 -!- DOMAIN: The C-terminus (approximately residues 1003-1170) is required
CC for interaction with M(2)S(1) and with Escherichia phage T7 Ocr
CC protein. {ECO:0000269|PubMed:32483229}.
CC -!- PTM: Upon purification after overexpression about one-third has the
CC initiating methionine removed. {ECO:0000269|PubMed:9033396}.
CC -!- MISCELLANEOUS: Type I restriction and modification enzymes are complex,
CC multifunctional systems which require ATP, S-adenosyl methionine and
CC magnesium as cofactors and, in addition to their endonucleolytic and
CC methylase activities, are potent DNA-dependent ATPases.
CC {ECO:0000269|PubMed:4868368, ECO:0000269|PubMed:9033396}.
CC -!- SIMILARITY: Belongs to the HsdR family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA97247.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE78340.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA29791.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA29791.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA38116.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X06545; CAA29791.1; ALT_SEQ; Genomic_DNA.
DR EMBL; U14003; AAA97247.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC77306.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE78340.1; ALT_INIT; Genomic_DNA.
DR EMBL; X54198; CAA38116.1; ALT_INIT; Genomic_DNA.
DR PIR; S56576; NDECKR.
DR RefSeq; NP_418770.2; NC_000913.3.
DR RefSeq; WP_000981388.1; NZ_LN832404.1.
DR AlphaFoldDB; P08956; -.
DR SMR; P08956; -.
DR BioGRID; 4262769; 27.
DR ComplexPortal; CPX-5628; Type I restriction-modification EcoKI complex.
DR DIP; DIP-9944N; -.
DR IntAct; P08956; 16.
DR STRING; 511145.b4350; -.
DR REBASE; 13380; EcoW3110ORF4339P.
DR REBASE; 152619; Rsp6212ORF1042P.
DR REBASE; 152623; Rsp621ORF1043P.
DR REBASE; 152628; Ret561ORF1035P.
DR REBASE; 152640; Rsp1341ORF1035P.
DR REBASE; 152652; Rsp113ORF1037P.
DR REBASE; 152690; Rph931ORF1047P.
DR REBASE; 152703; Rph831ORF1044P.
DR REBASE; 152713; Rsp741ORF1035P.
DR REBASE; 152735; Rsp871ORF1035P.
DR REBASE; 156145; BamRD77ORF2498P.
DR REBASE; 191895; Apa1447ORF2439P.
DR REBASE; 204158; Bli1441ORF2992P.
DR REBASE; 204718; Bsu333ORF2986P.
DR REBASE; 205028; Bve72ORF2738P.
DR REBASE; 205121; Bve1413ORF3003P.
DR REBASE; 441883; EcoBL21FORF4361P.
DR REBASE; 980; EcoKI.
DR TCDB; 3.A.17.1.1; the phage t7 injectisome (t7 injectisome) family.
DR PaxDb; P08956; -.
DR PRIDE; P08956; -.
DR EnsemblBacteria; AAC77306; AAC77306; b4350.
DR EnsemblBacteria; BAE78340; BAE78340; BAE78340.
DR GeneID; 948878; -.
DR KEGG; ecj:JW4313; -.
DR KEGG; eco:b4350; -.
DR PATRIC; fig|1411691.4.peg.2336; -.
DR EchoBASE; EB0454; -.
DR eggNOG; COG4096; Bacteria.
DR HOGENOM; CLU_007363_0_0_6; -.
DR InParanoid; P08956; -.
DR PhylomeDB; P08956; -.
DR BioCyc; EcoCyc:EG10459-MON; -.
DR BioCyc; MetaCyc:EG10459-MON; -.
DR BRENDA; 3.1.21.3; 2165.
DR PRO; PR:P08956; -.
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:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR GO; GO:0009035; F:type I site-specific deoxyribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0009307; P:DNA restriction-modification system; IDA:ComplexPortal.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR013670; EcoEI_R_C_dom.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR007409; Restrct_endonuc_type1_HsdR_N.
DR Pfam; PF08463; EcoEI_R_C; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF04313; HSDR_N; 1.
DR Pfam; PF04851; ResIII; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Coiled coil; Direct protein sequencing; DNA-binding;
KW Endonuclease; Helicase; Host-virus interaction; Hydrolase; Nuclease;
KW Nucleotide-binding; Reference proteome; Restriction system.
FT CHAIN 1..1170
FT /note="Type I restriction enzyme EcoKI endonuclease
FT subunit"
FT /id="PRO_0000077259"
FT DOMAIN 458..639
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 714..879
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT DNA_BIND 431..450
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT COILED 143..229
FT /evidence="ECO:0000255"
FT MOTIF 574..577
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 472..478
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 611..678
FT /note="DAVKIALTATPALHTVQIFGEPVYRYTYRTAVIDGFLIDQDPPIQIITRNAQ
FT EGVYLSKGEQVERISP -> ECGKNRSHRHPGATYCADFRRAGLPLYLPYRGYRRFSDR
FT PGSAYSDHHPQRAGGGLSLQRRAGRAH (in Ref. 1; CAA29791)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1170 AA; 134095 MW; C5B90A799C455318 CRC64;
MMNKSNFEFL KGVNDFTYAI ACAAENNYPD DPNTTLIKMR MFGEATAKHL GLLLNIPPCE
NQHDLLRELG KIAFVDDNIL SVFHKLRRIG NQAVHEYHND LNDAQMCLRL GFRLAVWYYR
LVTKDYDFPV PVFVLPERGE NLYHQEVLTL KQQLEQQVRE KAQTQAEVEA QQQKLVALNG
YIAILEGKQQ ETEAQTQARL AALEAQLAEK NAELAKQTEQ ERKAYHKEIT DQAIKRTLNL
SEEESRFLID AQLRKAGWQA DSKTLRFSKG ARPEPGVNKA IAEWPTGKDE TGNQGFADYV
LFVGLKPIAV VEAKRNNIDV PARLNESYRY SKCFDNGFLR ETLLEHYSPD EVHEAVPEYE
TSWQDTSGKQ RFKIPFCYST NGREYRATMK TKSGIWYRDV RDTRNMSKAL PEWHRPEELL
EMLGSEPQKQ NQWFADNPGM SELGLRYYQE DAVRAVEKAI VKGQQEILLA MATGTGKTRT
AIAMMFRLIQ SQRFKRILFL VDRRSLGEQA LGAFEDTRIN GDTFNSIFDI KGLTDKFPED
STKIHVATVQ SLVKRTLQSD EPMPVARYDC IVVDEAHRGY ILDKEQTEGE LQFRSQLDYV
SAYRRILDHF DAVKIALTAT PALHTVQIFG EPVYRYTYRT AVIDGFLIDQ DPPIQIITRN
AQEGVYLSKG EQVERISPQG EVINDTLEDD QDFEVADFNR GLVIPAFNRA VCNELTNYLD
PTGSQKTLVF CVTNAHADMV VEELRAAFKK KYPQLEHDAI IKITGDADKD ARKVQTMITR
FNKERLPNIV VTVDLLTTGV DIPSICNIVF LRKVRSRILY EQMKGRATRL CPEVNKTSFK
IFDCVDIYST LESVDTMRPV VVRPKVELQT LVNEITDSET YKITEADGRS FAEHSHEQLV
AKLQRIIGLA TFNRDRSETI DKQVRRLDEL CQDAAGVNFN GFASRLREKG PHWSAEVFNK
LPGFIARLEK LKTDINNLND APIFLDIDDE VVSVKSLYGD YDTPQDFLEA FDSLVQRSPN
AQPALQAVIN RPRDLTRKGL VELQEWFDRQ HFEESSLRKA WKETRNEDIA ARLIGHIRRA
AVGDALKPFE ERVDHALTRI KGENDWSSEQ LSWLDRLAQA LKEKVVLDDD VFKTGNFHRR
GGKAMLQRTF DDNLDTLLGK FSDYIWDELA
