T1R1_ECOLX
ID T1R1_ECOLX Reviewed; 1033 AA.
AC P10486;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Type I restriction enzyme EcoR124II endonuclease subunit {ECO:0000303|PubMed:12654995};
DE Short=EcoR124II {ECO:0000303|PubMed:12654995};
DE Short=R protein;
DE EC=3.1.21.3 {ECO:0000269|PubMed:32483229};
DE AltName: Full=Type I restriction enzyme EcoR124/3 endonuclease subunit {ECO:0000303|PubMed:2784505};
GN Name=hsdR {ECO:0000303|PubMed:2784505}; Synonyms=hsr;
OS Escherichia coli.
OG Plasmid IncFIV R124/3.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DNA RECOGNITION SITE.
RX PubMed=2784505; DOI=10.1016/0022-2836(89)90369-0;
RA Price C., Lingner J., Bickle J., Firman T.A., Glover S.W.;
RT "Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I
RT DNA restriction and modification enzymes.";
RL J. Mol. Biol. 205:115-125(1989).
RN [2]
RP NOMENCLATURE.
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:7BST, ECO:0007744|PDB:7BTO, ECO:0007744|PDB:7BTP, ECO:0007744|PDB:7BTQ, ECO:0007744|PDB:7BTR}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.97 ANGSTROMS) OF 1-1032 IN COMPLEX WITH
RP M AND S SUBUNITS AND WITH ESCHERICHIA PHAGE T7 PROTEIN OCR, FUNCTION,
RP CATALYTIC ACTIVITY, INTERACTION WITH ESCHERICHIA PHAGE T7 PROTEIN OCR
RP (MICROBIAL INFECTION), DOMAIN, DNA-BINDING, AND MUTAGENESIS OF
RP 43-ASP--GLY-48; 106-ASP--ASP-110; ASP-151; 248-PHE--HIS-251;
RP 288-LYS--THR-292; 720-GLY--SER-732; 859-ARG--GLN-886 AND 887-GLU--ALA-1038.
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 restriction (R) subunit of a type I restriction enzyme
CC that recognizes 5'-GAAN(7)RTCG-3' and cleaves a random distance away.
CC Subunit R is required for both nuclease and ATPase activities, but not
CC for modification (Probable) (PubMed:12654995). After locating an
CC unmethylated recognition site, the enzyme complex serves as a molecular
CC motor that translocates DNA in an ATP-dependent manner until a
CC collision occurs that triggers cleavage (Probable). The enzyme
CC undergoes major structural changes to bring the motor domains into
CC contact with DNA, allowing DNA translocation. This prevents DNA access
CC to the catalytic domains of both the R and M subunits, preventing both
CC restriction and methylation (PubMed:32483229).
CC {ECO:0000269|PubMed:32483229, ECO:0000303|PubMed:12654995,
CC ECO:0000305|PubMed:2784505, ECO:0000305|PubMed:32483229}.
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:32483229};
CC -!- SUBUNIT: The type I restriction/modification system is composed of
CC three polypeptides R, M and S; the restriction enzyme has stoichiometry
CC R(2)M(2)S(1) while the methyltransferase is M(2)S(1). There is an
CC equilibrium between R(2)M(2)S(1) and R(1)M(2)S(1); the latter is
CC methylation and translocation proficient but restriction deficient.
CC {ECO:0000269|PubMed:32483229}.
CC -!- SUBUNIT: (Microbial infection) Holoenenzyme interacts with Escherichia
CC phage T7 protein Ocr; this interaction leads to the inhibition of the
CC restriction activity, but may still allow methylation and
CC translocation. {ECO:0000269|PubMed:32483229}.
CC -!- DOMAIN: The individual domains assume different positions in the
CC enzyme, allowing the holoenzyme to regulate the methylase, endonuclease
CC and translocation states. Deletion of the linkers between the domains
CC prevents movelemt and thus restriction activity.
CC {ECO:0000269|PubMed:32483229}.
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:32483229}.
CC -!- SIMILARITY: Belongs to the HsdR family. {ECO:0000305}.
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DR EMBL; X13145; CAA31543.1; -; Genomic_DNA.
DR PIR; S02168; S02168.
DR PDB; 2W00; X-ray; 2.60 A; A/B=1-1032.
DR PDB; 4BE7; X-ray; 2.74 A; B/D=1-1032.
DR PDB; 4BEB; X-ray; 2.99 A; A/B/C/D=1-1032.
DR PDB; 4BEC; X-ray; 2.84 A; A/B=1-1032.
DR PDB; 4XJX; X-ray; 2.40 A; A/B=1-1032.
DR PDB; 5J3N; X-ray; 2.45 A; A/B=887-1032.
DR PDB; 6H2J; X-ray; 2.60 A; A/B=1-1032.
DR PDB; 7BST; EM; 4.37 A; B/C=1-1032.
DR PDB; 7BTO; EM; 3.97 A; C/F/G/H=1-1032.
DR PDB; 7BTP; EM; 4.01 A; A=1-1032.
DR PDB; 7BTQ; EM; 4.54 A; F=1-1032.
DR PDB; 7BTR; EM; 4.54 A; C=1-1032.
DR PDBsum; 2W00; -.
DR PDBsum; 4BE7; -.
DR PDBsum; 4BEB; -.
DR PDBsum; 4BEC; -.
DR PDBsum; 4XJX; -.
DR PDBsum; 5J3N; -.
DR PDBsum; 6H2J; -.
DR PDBsum; 7BST; -.
DR PDBsum; 7BTO; -.
DR PDBsum; 7BTP; -.
DR PDBsum; 7BTQ; -.
DR PDBsum; 7BTR; -.
DR AlphaFoldDB; P10486; -.
DR SMR; P10486; -.
DR DIP; DIP-17005N; -.
DR REBASE; 391271; Eco6193ORF160P.
DR REBASE; 989; EcoR124II.
DR REBASE; 990; EcoR124I.
DR BRENDA; 3.1.21.3; 2026.
DR EvolutionaryTrace; P10486; -.
DR PRO; PR:P10486; -.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; 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; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR007409; Restrct_endonuc_type1_HsdR_N.
DR InterPro; IPR004473; Restrct_endonuc_typeI_HsdR.
DR InterPro; IPR040980; SWI2_SNF2.
DR InterPro; IPR022625; TypeI_RM_Rsu_C.
DR Pfam; PF12008; EcoR124_C; 1.
DR Pfam; PF04313; HSDR_N; 1.
DR Pfam; PF18766; SWI2_SNF2; 1.
DR SMART; SM00487; DEXDc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00348; hsdR; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Endonuclease; Hydrolase; Nuclease;
KW Nucleotide-binding; Plasmid; Restriction system.
FT CHAIN 1..1033
FT /note="Type I restriction enzyme EcoR124II endonuclease
FT subunit"
FT /id="PRO_0000077260"
FT DOMAIN 294..456
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT REGION 31..249
FT /note="Nuclease domain"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 250..469
FT /note="Motor 1 domain"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 470..702
FT /note="Motor 2 domain"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 720..732
FT /note="Motor 2-helicase linker"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 732..860
FT /note="Helicase domain"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 859..886
FT /note="Helicase-CTD linker"
FT /evidence="ECO:0000305|PubMed:32483229"
FT REGION 886..1033
FT /note="C-terminal domain"
FT /evidence="ECO:0000305|PubMed:32483229"
FT BINDING 308..314
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MUTAGEN 43..48
FT /note="DLRNQG->ALRAAA: Holoenzyme assembles, some
FT impairment of restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 106..110
FT /note="DYICD->AAACA: Significantly decreased binding to
FT M(2)S(1), loss of restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 151
FT /note="D->A: Loss of DNA restriction."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 248..251
FT /note="FQKH->AAAA: Holoenzyme assembles, loss of
FT restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 288..292
FT /note="KSSFT->AAAAA: Holoenzyme assembly is impaired, some
FT impairment of restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 720..732
FT /note="Missing: Loss of restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 859..886
FT /note="Missing: Loss of restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT MUTAGEN 887..1033
FT /note="Missing: Significantly decreased binding to
FT M(2)S(1), significantly decreased binding to Ocr, loss of
FT restriction activity."
FT /evidence="ECO:0000269|PubMed:32483229"
FT HELIX 33..46
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 57..72
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 118..124
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 126..128
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 134..138
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:4BEB"
FT STRAND 151..156
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 159..166
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 173..180
FT /evidence="ECO:0007829|PDB:4XJX"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 193..197
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 200..204
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 209..213
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 240..246
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 260..263
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 274..292
FT /evidence="ECO:0007829|PDB:4XJX"
FT TURN 299..301
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 302..307
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 313..324
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 332..337
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 344..351
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 359..361
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 365..371
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 378..382
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 383..392
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 397..400
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 401..409
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 412..414
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 415..425
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 427..437
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 441..443
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 450..454
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 456..461
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 463..468
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 475..479
FT /evidence="ECO:0007829|PDB:4XJX"
FT TURN 484..486
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 487..490
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 495..500
FT /evidence="ECO:0007829|PDB:4XJX"
FT TURN 504..508
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 510..527
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 531..534
FT /evidence="ECO:0007829|PDB:2W00"
FT STRAND 539..546
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 547..566
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 568..570
FT /evidence="ECO:0007829|PDB:2W00"
FT STRAND 576..579
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 586..589
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 591..593
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 601..603
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 606..623
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 631..646
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 649..657
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 660..662
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 668..675
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 679..686
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 687..689
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 699..706
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 709..718
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 724..728
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 733..738
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 739..741
FT /evidence="ECO:0007829|PDB:4BEB"
FT TURN 743..745
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 748..750
FT /evidence="ECO:0007829|PDB:4BEB"
FT HELIX 752..762
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 766..769
FT /evidence="ECO:0007829|PDB:2W00"
FT HELIX 772..792
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 796..804
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 811..813
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 818..821
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 826..832
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 840..852
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 880..883
FT /evidence="ECO:0007829|PDB:4XJX"
FT STRAND 884..886
FT /evidence="ECO:0007829|PDB:4XJX"
FT HELIX 887..899
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 909..920
FT /evidence="ECO:0007829|PDB:5J3N"
FT STRAND 921..923
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 925..927
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 928..936
FT /evidence="ECO:0007829|PDB:5J3N"
FT TURN 940..942
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 946..971
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 976..989
FT /evidence="ECO:0007829|PDB:5J3N"
FT TURN 996..999
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 1000..1002
FT /evidence="ECO:0007829|PDB:5J3N"
FT STRAND 1012..1014
FT /evidence="ECO:0007829|PDB:5J3N"
FT HELIX 1016..1031
FT /evidence="ECO:0007829|PDB:5J3N"
SQ SEQUENCE 1033 AA; 119657 MW; B55F3991356C1506 CRC64;
MTHQTHTIAE SNNFIVLDKY IKAEPTGDSY QSESDLEREL IQDLRNQGYE FISVKSQSAM
LANVREQLQN LNGVVFNDSE WRRFTEQYLD NPSDGILDKT RKIHIDYICD FIFDDERLEN
IYLIDKKNLM RNKVQIIQQF EQAGSHANRY DVTILVNGLP LVQIELKKRG VAIREAFNQI
HRYSKESFNS ENSLFKYLQL FVISNGTDTR YFANTTKRDK NSFDFTMNWA KSDNTLIKDL
KDFTATCFQK HTLLNVLVNY SVFDSSQTLL VMRPYQIAAT ERILWKIKSS FTAKNWSKPE
SGGYIWHTTG SGKTLTSFKA ARLATELDFI DKVFFVVDRK DLDYQTMKEY QRFSPDSVNG
SENTAGLKRN LDKDDNKIIV TTIQKLNNLM KAESDLPVYN QQVVFIFDEC HRSQFGEAQK
NLKKKFKRYY QFGFTGTPIF PENALGSETT ASVFGRELHS YVITDAIRDE KVLKFKVDYN
DVRPQFKSLE TETDEKKLSA AENQQAFLHP MRIQEITQYI LNNFRQKTHR TFPGSKGFNA
MLAVSSVDAA KAYYATFKRL QEEAANKSAT YKPLRIATIF SFAANEEQNA IGEISDETFD
TSAMDSSAKE FLDAAIREYN SHFKTNFSTD SNGFQNYYRD LAQRVKNQDI DLLIVVGMFL
TGFDAPTLNT LFVDKNLRYH GLMQAFSRTN RIYDATKTFG NIVTFRDLER STIDAITLFG
DKNTKNVVLE KSYTEYMEGF TDAATGEAKR GFMTVVSELE QRFPDPTSIE SEKEKKDFVK
LFGEYLRAEN ILQNYDEFAT LKALQQIDLS DPVAVEKFKA EHYVDDEKFA ELQTIRLPAD
RKIQDYRSAY NDIRDWQRRE KEAEKKEKST TDWDDVVFEV DLLKSQEINL DYILGLIFEH
NRQNKGKGEM IEEVKRLIRS SLGNRAKEGL VVDFIQQTNL DDLPDKASII DAFFTFAQRE
QQREAEALIK EENLNEDAAK RYIRTSLKRE YATENGTELN ETLPKLSPLN PQYKTKKQAV
FRKSSRLLRS LKA
