DNE1_CHLRE
ID DNE1_CHLRE Reviewed; 163 AA.
AC P05725;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=DNA endonuclease I-CreI;
DE EC=3.1.-.-;
DE AltName: Full=23S rRNA intron protein;
OS Chlamydomonas reinhardtii (Chlamydomonas smithii).
OG Plastid; Chloroplast.
OC Eukaryota; Viridiplantae; Chlorophyta; core chlorophytes; Chlorophyceae;
OC CS clade; Chlamydomonadales; Chlamydomonadaceae; Chlamydomonas.
OX NCBI_TaxID=3055;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=4000933; DOI=10.1093/nar/13.3.975;
RA Rochaix J.-D., Rahire M., Michel F.;
RT "The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a
RT polypeptide related to mitochondrial maturases.";
RL Nucleic Acids Res. 13:975-984(1985).
RN [2]
RP SEQUENCE REVISION TO 42; 110 AND 111.
RA Monnat R.J.;
RL Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP CHARACTERIZATION.
RX PubMed=1398106; DOI=10.1016/0378-1119(92)90278-w;
RA Thompson A.J., Yuan X., Kudlicki W., Herin D.L.;
RT "Cleavage and recognition pattern of a double-strand-specific endonuclease
RT (I-CreI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas
RT reinhardtii.";
RL Gene 119:247-251(1992).
RN [4]
RP CHARACTERIZATION.
RX PubMed=8437585; DOI=10.1007/bf00277141;
RA Duerrenberger F., Rochaix J.-D.;
RT "Characterization of the cleavage site and the recognition sequence of the
RT I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of
RT Chlamydomonas reinhardtii.";
RL Mol. Gen. Genet. 236:409-414(1993).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=9187655; DOI=10.1038/nsb0697-468;
RA Heath P.J., Stephens K.M., Monnat R.J. Jr., Stoddard B.L.;
RT "The structure of I-CreI, a group I intron-encoded homing endonuclease.";
RL Nat. Struct. Biol. 4:468-476(1997).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 2-153 IN COMPLEX WITH DIVALENT
RP METAL CATIONS, COFACTOR, AND SUBUNIT.
RX PubMed=11276249; DOI=10.1038/86181;
RA Chevalier B.S., Monnat R.J. Jr., Stoddard B.L.;
RT "The homing endonuclease I-CreI uses three metals, one of which is shared
RT between the two active sites.";
RL Nat. Struct. Biol. 8:312-316(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 9-163 IN COMPLEX WITH DNA AND
RP DIVALENT METAL CATIONS, SUBUNIT, AND MUTAGENESIS.
RX PubMed=12419232; DOI=10.1016/s1097-2765(02)00690-1;
RA Chevalier B.S., Kortemme T., Chadsey M.S., Baker D., Monnat R.J.,
RA Stoddard B.L.;
RT "Design, activity, and structure of a highly specific artificial
RT endonuclease.";
RL Mol. Cell 10:895-905(2002).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL
RP CATIONS, SUBUNIT, AND COFACTOR.
RX PubMed=12758074; DOI=10.1016/s0022-2836(03)00447-9;
RA Chevalier B., Turmel M., Lemieux C., Monnat R.J. Jr., Stoddard B.L.;
RT "Flexible DNA target site recognition by divergent homing endonuclease
RT isoschizomers I-CreI and I-MsoI.";
RL J. Mol. Biol. 329:253-269(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANTS ASN-20 AND GLU-47 IN
RP COMPLEX WITH CALCIUM IONS AND DNA, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
RP ASP-20; GLN-47 AND LYS-98.
RX PubMed=15518550; DOI=10.1021/bi048970c;
RA Chevalier B., Sussman D., Otis C., Noel A.-J., Turmel M., Lemieux C.,
RA Stephens K., Monnat R.J. Jr., Stoddard B.L.;
RT "Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing
RT endonuclease.";
RL Biochemistry 43:14015-14026(2004).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH DNA, SUBUNIT, AND
RP MUTAGENESIS OF GLN-26 AND TYR-33.
RX PubMed=15313605; DOI=10.1016/j.jmb.2004.07.031;
RA Sussman D., Chadsey M., Fauce S., Engel A., Bruett A., Monnat R. Jr.,
RA Stoddard B.L., Seligman L.M.;
RT "Isolation and characterization of new homing endonuclease specificities at
RT individual target site positions.";
RL J. Mol. Biol. 342:31-41(2004).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-153 IN COMPLEX WITH DNA,
RP SUBUNIT, AND MUTAGENESIS OF TYR-33; GLN-44 AND ARG-68.
RX PubMed=16971456; DOI=10.1093/nar/gkl645;
RA Rosen L.E., Morrison H.A., Masri S., Brown M.J., Springstubb B.,
RA Sussman D., Stoddard B.L., Seligman L.M.;
RT "Homing endonuclease I-CreI derivatives with novel DNA target
RT specificities.";
RL Nucleic Acids Res. 34:4791-4800(2006).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-156 IN COMPLEX WITH DNA,
RP SUBUNIT, AND MUTAGENESIS OF SER-138; LYS-139; LYS-142 AND THR-143.
RX PubMed=17452357; DOI=10.1093/nar/gkm183;
RA Prieto J., Redondo P., Padro D., Arnould S., Epinat J.-C., Paques F.,
RA Blanco F.J., Montoya G.;
RT "The C-terminal loop of the homing endonuclease I-CreI is essential for
RT site recognition, DNA binding and cleavage.";
RL Nucleic Acids Res. 35:3262-3271(2007).
CC -!- FUNCTION: Endonuclease involved in group I intron homing. Recognizes
CC and cleaves a 19-24 bp palindromic DNA site.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC Note=Binds 3 Mg(2+) ions per homodimer. The enzyme can also utilize
CC Mn(2+) or Co(2+), but has lower cleavage activity with Ni(2+) or
CC Zn(2+). Ca(2+) Co(2+) give no enzyme activity.
CC {ECO:0000269|PubMed:11276249, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15518550};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11276249,
CC ECO:0000269|PubMed:12419232, ECO:0000269|PubMed:12758074,
CC ECO:0000269|PubMed:15313605, ECO:0000269|PubMed:15518550,
CC ECO:0000269|PubMed:16971456, ECO:0000269|PubMed:17452357}.
CC -!- INTERACTION:
CC P05725; P05725: -; NbExp=5; IntAct=EBI-15738760, EBI-15738760;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- SIMILARITY: Belongs to the LAGLIDADG endonuclease family.
CC {ECO:0000305}.
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DR EMBL; X01977; CAA26008.2; -; Genomic_DNA.
DR PIR; A23091; A23091.
DR PDB; 1AF5; X-ray; 3.00 A; A=4-138.
DR PDB; 1BP7; X-ray; 3.00 A; A/B/C/D=2-153.
DR PDB; 1G9Y; X-ray; 2.05 A; A/B=2-153.
DR PDB; 1G9Z; X-ray; 1.80 A; A/B=2-153.
DR PDB; 1MOW; X-ray; 2.40 A; A/D/G/J=17-163.
DR PDB; 1N3E; X-ray; 2.50 A; A/B/G/H=1-163.
DR PDB; 1N3F; X-ray; 2.00 A; A/B/G/H=1-163.
DR PDB; 1T9I; X-ray; 1.60 A; A/B=1-163.
DR PDB; 1T9J; X-ray; 2.00 A; A/B=1-163.
DR PDB; 1U0C; X-ray; 2.50 A; A/B=1-163.
DR PDB; 1U0D; X-ray; 2.90 A; A/B=1-163.
DR PDB; 2I3P; X-ray; 2.30 A; A/B=1-153.
DR PDB; 2I3Q; X-ray; 2.30 A; A/B=1-153.
DR PDB; 2O7M; X-ray; 2.00 A; A/B=1-156.
DR PDB; 2VBJ; X-ray; 1.95 A; A/B=2-153.
DR PDB; 2VBL; X-ray; 1.80 A; A/B=1-153.
DR PDB; 2VBN; X-ray; 1.90 A; A/B=1-153.
DR PDB; 2VBO; X-ray; 1.80 A; A/B=1-153.
DR PDB; 4AAB; X-ray; 2.50 A; A/B=2-153.
DR PDB; 4AAD; X-ray; 3.10 A; A/B=2-153.
DR PDB; 4AAE; X-ray; 2.60 A; A/B=2-154.
DR PDB; 4AAF; X-ray; 2.50 A; A/B=2-153.
DR PDB; 4AAG; X-ray; 2.80 A; A/B=2-153.
DR PDB; 4AQU; X-ray; 2.30 A; A/B=2-153.
DR PDB; 4AQX; X-ray; 2.20 A; A/B=2-153.
DR PDB; 6FB0; X-ray; 2.15 A; A=2-154, B=2-155.
DR PDB; 6FB1; X-ray; 3.02 A; A/B=2-155.
DR PDB; 6FB2; X-ray; 2.95 A; A=2-154, B=2-155.
DR PDB; 6FB5; X-ray; 2.20 A; A=2-154, B=2-155.
DR PDB; 6FB6; X-ray; 2.60 A; A=2-154, B=2-155.
DR PDB; 6FB7; X-ray; 2.69 A; A/B=2-153.
DR PDB; 6FB8; X-ray; 2.45 A; A/B=2-153.
DR PDB; 6FB9; X-ray; 2.95 A; A/B=2-153.
DR PDBsum; 1AF5; -.
DR PDBsum; 1BP7; -.
DR PDBsum; 1G9Y; -.
DR PDBsum; 1G9Z; -.
DR PDBsum; 1MOW; -.
DR PDBsum; 1N3E; -.
DR PDBsum; 1N3F; -.
DR PDBsum; 1T9I; -.
DR PDBsum; 1T9J; -.
DR PDBsum; 1U0C; -.
DR PDBsum; 1U0D; -.
DR PDBsum; 2I3P; -.
DR PDBsum; 2I3Q; -.
DR PDBsum; 2O7M; -.
DR PDBsum; 2VBJ; -.
DR PDBsum; 2VBL; -.
DR PDBsum; 2VBN; -.
DR PDBsum; 2VBO; -.
DR PDBsum; 4AAB; -.
DR PDBsum; 4AAD; -.
DR PDBsum; 4AAE; -.
DR PDBsum; 4AAF; -.
DR PDBsum; 4AAG; -.
DR PDBsum; 4AQU; -.
DR PDBsum; 4AQX; -.
DR PDBsum; 6FB0; -.
DR PDBsum; 6FB1; -.
DR PDBsum; 6FB2; -.
DR PDBsum; 6FB5; -.
DR PDBsum; 6FB6; -.
DR PDBsum; 6FB7; -.
DR PDBsum; 6FB8; -.
DR PDBsum; 6FB9; -.
DR AlphaFoldDB; P05725; -.
DR SMR; P05725; -.
DR DIP; DIP-59771N; -.
DR REBASE; 2540; I-CreI.
DR EvolutionaryTrace; P05725; -.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR Gene3D; 3.10.28.10; -; 1.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR004860; LAGLIDADG_2.
DR Pfam; PF00961; LAGLIDADG_1; 1.
DR SUPFAM; SSF55608; SSF55608; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Endonuclease; Hydrolase; Intron homing;
KW Magnesium; Metal-binding; Nuclease; Plastid.
FT CHAIN 1..163
FT /note="DNA endonuclease I-CreI"
FT /id="PRO_0000192783"
FT REGION 26..38
FT /note="Interaction with DNA"
FT REGION 44..47
FT /note="Interaction with DNA"
FT REGION 68..70
FT /note="Interaction with DNA"
FT REGION 138..143
FT /note="Interaction with DNA"
FT BINDING 19
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 20
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT BINDING 20
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared between dimeric partners"
FT MUTAGEN 20
FT /note="D->A,L,N: Loss of catalytic activity. Reduced
FT affinity for DNA."
FT /evidence="ECO:0000269|PubMed:15518550"
FT MUTAGEN 26
FT /note="Q->A,C: Alters the specificity of the endonuclease."
FT /evidence="ECO:0000269|PubMed:15313605"
FT MUTAGEN 33
FT /note="Y->C,H,R: Alters the specificity of the
FT endonuclease."
FT /evidence="ECO:0000269|PubMed:15313605,
FT ECO:0000269|PubMed:16971456"
FT MUTAGEN 44
FT /note="Q->A,C,T,V,W: Alters the specificity of the
FT endonuclease."
FT /evidence="ECO:0000269|PubMed:16971456"
FT MUTAGEN 47
FT /note="Q->A,E,M: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:15518550"
FT MUTAGEN 47
FT /note="Q->N: Strongly reduced affinity for DNA. No effect
FT on catalytic activity."
FT /evidence="ECO:0000269|PubMed:15518550"
FT MUTAGEN 68
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16971456"
FT MUTAGEN 98
FT /note="K->A: Strongly reduced affinity for DNA. Increased
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:15518550"
FT MUTAGEN 98
FT /note="K->R: Strongly reduced affinity for DNA. No effect
FT on catalytic activity."
FT /evidence="ECO:0000269|PubMed:15518550"
FT MUTAGEN 138
FT /note="S->A: Reduced affinity for DNA. No effect on
FT catalytic activity. Reduced cleavage; when associated with
FT M-139."
FT /evidence="ECO:0000269|PubMed:17452357"
FT MUTAGEN 139
FT /note="K->M: Reduced affinity for DNA. No effect on
FT catalytic activity. Reduced cleavage; when associated with
FT A-138."
FT /evidence="ECO:0000269|PubMed:17452357"
FT MUTAGEN 142
FT /note="K->G: Reduced affinity for DNA. No effect on
FT catalytic activity. Reduced cleavage; when associated with
FT G-143."
FT /evidence="ECO:0000269|PubMed:17452357"
FT MUTAGEN 143
FT /note="T->G: Reduced affinity for DNA. No effect on
FT catalytic activity. Reduced cleavage; when associated with
FT G-142."
FT /evidence="ECO:0000269|PubMed:17452357"
FT HELIX 7..20
FT /evidence="ECO:0007829|PDB:1T9I"
FT STRAND 22..29
FT /evidence="ECO:0007829|PDB:1T9I"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:1U0D"
FT STRAND 36..48
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 52..62
FT /evidence="ECO:0007829|PDB:1T9I"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:1T9I"
FT STRAND 73..78
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 81..91
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:1T9I"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 99..115
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 119..135
FT /evidence="ECO:0007829|PDB:1T9I"
FT HELIX 145..153
FT /evidence="ECO:0007829|PDB:1T9I"
SQ SEQUENCE 163 AA; 18696 MW; 22B625C0CD72F575 CRC64;
MNTKYNKEFL LYLAGFVDGD GSIIAQIKPN QSYKFKHQLS LTFQVTQKTQ RRWFLDKLVD
EIGVGYVRDR GSVSDYILSE IKPLHNFLTQ LQPFLKLKQK QANLVLKIIE QLPSAKESPD
KFLEVCTWVD QIAALNDSKT RKTTSETVRA VLDSLSEKKK SSP
