T3RE_ECOLX
ID T3RE_ECOLX Reviewed; 970 AA.
AC Q5ZND2;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=Type III restriction-modification enzyme EcoP15I Res subunit {ECO:0000303|PubMed:15464603};
DE EC=3.1.21.5 {ECO:0000269|PubMed:11178902};
DE AltName: Full=Type III restriction enzyme EcoP15I {ECO:0000303|PubMed:12654995};
GN Name=res {ECO:0000303|PubMed:15464603};
GN Synonyms=ecoP15Ires {ECO:0000303|PubMed:15464603};
OS Escherichia coli.
OG Plasmid p15B.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC PLASMID=p15B;
RX PubMed=15464603; DOI=10.1016/j.jbiotec.2004.06.014;
RA Moencke-Buchner E., Mackeldanz P., Krueger D.H., Reuter M.;
RT "Overexpression and affinity chromatography purification of the Type III
RT restriction endonuclease EcoP15I for use in transcriptome analysis.";
RL J. Biotechnol. 114:99-106(2004).
RN [2]
RP FUNCTION, SUBSTRATE SPECIFICITY, CATALYTIC ACTIVITY, AND SUBUNIT.
RC PLASMID=p15B;
RX PubMed=11178902; DOI=10.1006/jmbi.2000.4411;
RA Janscak P., Sandmeier U., Szczelkun M.D., Bickle T.A.;
RT "Subunit assembly and mode of DNA cleavage of the type III restriction
RT endonucleases EcoP1I and EcoP15I.";
RL J. Mol. Biol. 306:417-431(2001).
RN [3]
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 [4] {ECO:0007744|PDB:4ZCF}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH MOD; AMP AND DNA,
RP AND DOMAIN.
RX PubMed=26067164; DOI=10.1038/ncomms8363;
RA Gupta Y.K., Chan S.H., Xu S.Y., Aggarwal A.K.;
RT "Structural basis of asymmetric DNA methylation and ATP-triggered long-
RT range diffusion by EcoP15I.";
RL Nat. Commun. 6:7363-7363(2015).
CC -!- FUNCTION: A type III restriction enzyme that recognizes 2 inversely
CC oriented double-stranded sequences 5'-CAGCAG-3' and cleaves DNA 25-27
CC base pairs downstream of one site. DNA restriction requires both the
CC Res and Mod subunits (PubMed:11178902, PubMed:15464603). DNA topology
CC affects its action; relaxed and negatively supercoiled DNA are digested
CC but positively supercoiled DNA is not a good substrate
CC (PubMed:11178902). Interacts with DNA approximately one half-turn
CC downstream of the recognition site (PubMed:26067164). After binding to
CC one recognition site undergoes random one-dimensional diffusion along
CC DNA until it collides with a stationary enzyme bound to the second DNA
CC site, which is when DNA cleavage occurs (Probable).
CC {ECO:0000269|PubMed:11178902, ECO:0000269|PubMed:15464603,
CC ECO:0000269|PubMed:26067164, ECO:0000305|PubMed:26067164}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of DNA to give specific double-
CC stranded fragments with terminal 5'-phosphates.; EC=3.1.21.5;
CC Evidence={ECO:0000269|PubMed:11178902};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC -!- COFACTOR:
CC Name=S-adenosyl-L-methionine; Xref=ChEBI:CHEBI:59789;
CC Evidence={ECO:0000250|UniProtKB:P08764};
CC -!- SUBUNIT: A heterotetramer with stoichiometry Res(2)Mod(2)
CC (PubMed:11178902). A heterotrimer with stoichiometry Res(1)Mod(2)
CC (PubMed:26067164). {ECO:0000269|PubMed:11178902,
CC ECO:0000269|PubMed:26067164}.
CC -!- DOMAIN: Has a helicase-type domain in its N-terminus and an
CC endonuclease-type domain in its C-terminus. AMP lies in a cleft in the
CC helicase domain. {ECO:0000269|PubMed:26067164, ECO:0007744|PDB:4ZCF}.
CC -!- SIMILARITY: Belongs to the type III restriction-modification system Res
CC protein family. {ECO:0000305}.
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DR EMBL; AJ634453; CAG24073.1; -; Genomic_DNA.
DR RefSeq; WP_001569359.1; NZ_UEMP01000032.1.
DR PDB; 4ZCF; X-ray; 2.60 A; C=1-970.
DR PDBsum; 4ZCF; -.
DR SMR; Q5ZND2; -.
DR REBASE; 987; EcoP15I.
DR PATRIC; fig|562.6968.peg.3407; -.
DR BRENDA; 3.1.21.4; 2026.
DR BRENDA; 3.1.21.5; 2026.
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:0015668; F:type III site-specific deoxyribonuclease activity; IEA:InterPro.
DR GO; GO:0009307; P:DNA restriction-modification system; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR045572; RE_endonuc_C.
DR Pfam; PF19778; RE_endonuc; 1.
DR Pfam; PF04851; ResIII; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Endonuclease; Helicase; Hydrolase;
KW Nuclease; Nucleotide-binding; Plasmid; Restriction system;
KW S-adenosyl-L-methionine.
FT CHAIN 1..970
FT /note="Type III restriction-modification enzyme EcoP15I Res
FT subunit"
FT /id="PRO_0000454399"
FT REGION 75..540
FT /note="Helicase-like domain"
FT /evidence="ECO:0000269|PubMed:26067164"
FT REGION 894..918
FT /note="Endonuclease domain"
FT /evidence="ECO:0000269|PubMed:26067164"
FT BINDING 91
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:26067164,
FT ECO:0007744|PDB:4ZCF"
FT BINDING 122
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:26067164,
FT ECO:0007744|PDB:4ZCF"
FT BINDING 126
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:26067164,
FT ECO:0007744|PDB:4ZCF"
FT BINDING 226
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:26067164,
FT ECO:0007744|PDB:4ZCF"
FT HELIX 12..22
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 36..41
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 50..64
FT /evidence="ECO:0007829|PDB:4ZCF"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 79..84
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 90..105
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 109..113
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 117..128
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 130..140
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 143..148
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 165..172
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 180..186
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 188..191
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:4ZCF"
FT TURN 205..208
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 212..217
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 222..227
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 236..242
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 249..254
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 261..267
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 269..274
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 280..285
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 320..322
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 331..333
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 338..341
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 347..349
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 363..366
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 368..389
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 399..404
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 421..434
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 445..455
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 459..461
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 475..483
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 485..488
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 497..501
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 502..507
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 513..518
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 528..532
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 533..535
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 553..558
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 565..576
FT /evidence="ECO:0007829|PDB:4ZCF"
FT TURN 588..590
FT /evidence="ECO:0007829|PDB:4ZCF"
FT STRAND 591..593
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 621..632
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 670..675
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 688..701
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 745..756
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 760..769
FT /evidence="ECO:0007829|PDB:4ZCF"
FT HELIX 782..798
FT /evidence="ECO:0007829|PDB:4ZCF"
SQ SEQUENCE 970 AA; 110957 MW; 43EE1DB3C115A20A CRC64;
MSKGFTLEKN LPHQKAGVDA VMNVFVSATP HLTDNVAVRL LANPELKLSE QQYYNNIKNV
QAFNGIAHSK DNHNAKSNII DVSMETGTGK TYTYIKTIFD LNKSFGINKF IIIVPTLSIK
AGTVNFLKSD ALKEHFRDDY KRELRTYVVE SQKNAGKNTK SYMPQAIHDF VEASNFNKKY
IHVLVINSGM INSKSLTDTY DTGLLDNQFN TPVDALRAVK PFIIIDEPHR FPTGKKTWEN
IEKFNAQYII RYGATFSEGY KNLVYRLTAV DAFNDDLVKG IDAYIEDIVG DGNANLKFVK
SDGKEATFEL NENNNKKSFK LAKGESLSKT HSAIHDLTLD ALNKSTAVLS NGIELKIGSS
INPYSYDQTL ADNMMRKAVK EHFKLEKELL TQRPRIKPLT LFFIDDIEGY RDGNDISGSL
KTKFEEYVLA EANELLKTEQ DAFYKNYLEK TVTNISSVHG GYFSKDNSDK DDKIEQEINE
ILHDKELLLS LDNPRRFIFS KWTLREGWDN PNVFQICKLR SSGSTTSKLQ EVGRGLRLPV
NEYMCRVKDR NFTLKYYVDF TEKDFVDSLV KEVNESSFKE RVPSKFTQEL KEQIMAQYPE
LSSRALMNEL FNDEIIDDND NFKDSDAYSR LKSKYPAAFP IGVKPGKIKK ATDGKRRTKM
RVGKFSELKE LWDLINQKAV IEYKINSESE FLSIFKSFML EETERFTKSG VHTRIDKIYI
HNDMAMSKSI VSDDDDFAKL NTMSYREFLD NLSQTIFVKH GTLHKVFCDI KDTINITEYL
NIQTIRKIKS GFSKYLLNNS FNKFSLGYNL ISGSIHPTKF TNADGNPLGE VLSSDLGVLQ
DNAKAPLDTY LFEEVFYDSE LERRNITDRE IQSVVVFSKI PKNSIKIPVA GGYTYSPDFA
YVVKTAEGDY LNFIIETKNV DSKDSLRLEE KRKIEHAQAL FNQISQSVKV EFRTQFANDD
IYQLIKSALP
