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   24-JAN-2024, entry version 193.
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; Pseudomonadota; 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; 511145-b4350; -.
DR   EnsemblBacteria; AAC77306; AAC77306; b4350.
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-MONOMER; -.
DR   BioCyc; MetaCyc:EG10459-MONOMER; -.
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   CDD; cd18032; DEXHc_RE_I_III_res; 1.
DR   CDD; cd18799; SF2_C_EcoAI-like; 1.
DR   Gene3D; 3.90.1570.30; -; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 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   PANTHER; PTHR47396:SF1; ATP-DEPENDENT HELICASE IRC3-RELATED; 1.
DR   PANTHER; PTHR47396; TYPE I RESTRICTION ENZYME ECOKI R PROTEIN; 1.
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; P-loop containing nucleoside triphosphate hydrolases; 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
//