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Protein

DNA endonuclease I-CreI

Gene
N/A
Organism
Chlamydomonas reinhardtii (Chlamydomonas smithii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endonuclease involved in group I intron homing. Recognizes and cleaves a 19-24 bp palindromic DNA site.

Cofactori

Mg2+3 Publications, Mn2+3 Publications, Co2+3 Publications, Ni2+3 Publications, Zn2+3 PublicationsNote: Binds 3 Mg2+ ions per homodimer. The enzyme can also utilize Mn2+ or Co2+, but has lower cleavage activity with Ni2+ or Zn2+. Ca2+ Co2+ give no enzyme activity.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi19 – 191Magnesium 1; via carbonyl oxygen
Metal bindingi20 – 201Magnesium 1
Metal bindingi20 – 201Magnesium 2; shared with dimeric partner

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Intron homing

Keywords - Ligandi

Magnesium, Metal-binding

Protein family/group databases

REBASEi2540. I-CreI.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA endonuclease I-CreI (EC:3.1.-.-)
Alternative name(s):
23S rRNA intron protein
Encoded oniPlastid; Chloroplast
OrganismiChlamydomonas reinhardtii (Chlamydomonas smithii)
Taxonomic identifieri3055 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeChlorophytaChlorophyceaeChlamydomonadalesChlamydomonadaceaeChlamydomonas

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi20 – 201D → A, L or N: Loss of catalytic activity. Reduced affinity for DNA. 1 Publication
Mutagenesisi26 – 261Q → A or C: Alters the specificity of the endonuclease. 1 Publication
Mutagenesisi33 – 331Y → C, H or R: Alters the specificity of the endonuclease. 2 Publications
Mutagenesisi44 – 441Q → A, C, T, V or W: Alters the specificity of the endonuclease. 1 Publication
Mutagenesisi47 – 471Q → A, E or M: Loss of catalytic activity. 1 Publication
Mutagenesisi47 – 471Q → N: Strongly reduced affinity for DNA. No effect on catalytic activity. 1 Publication
Mutagenesisi68 – 681R → A: Loss of activity. 1 Publication
Mutagenesisi98 – 981K → A: Strongly reduced affinity for DNA. Increased catalytic activity. 1 Publication
Mutagenesisi98 – 981K → R: Strongly reduced affinity for DNA. No effect on catalytic activity. 1 Publication
Mutagenesisi138 – 1381S → A: Reduced affinity for DNA. No effect on catalytic activity. Reduced cleavage; when associated with M-139. 1 Publication
Mutagenesisi139 – 1391K → M: Reduced affinity for DNA. No effect on catalytic activity. Reduced cleavage; when associated with A-138. 1 Publication
Mutagenesisi142 – 1421K → G: Reduced affinity for DNA. No effect on catalytic activity. Reduced cleavage; when associated with G-143. 1 Publication
Mutagenesisi143 – 1431T → G: Reduced affinity for DNA. No effect on catalytic activity. Reduced cleavage; when associated with G-142. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 163163DNA endonuclease I-CreIPRO_0000192783Add
BLAST

Interactioni

Subunit structurei

Homodimer.7 Publications

Protein-protein interaction databases

DIPiDIP-59771N.

Structurei

Secondary structure

1
163
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 2014Combined sources
Beta strandi22 – 298Combined sources
Beta strandi31 – 333Combined sources
Beta strandi36 – 4813Combined sources
Helixi49 – 513Combined sources
Helixi52 – 6211Combined sources
Beta strandi66 – 705Combined sources
Beta strandi73 – 786Combined sources
Helixi81 – 9111Combined sources
Helixi92 – 943Combined sources
Beta strandi96 – 983Combined sources
Helixi99 – 11517Combined sources
Helixi119 – 13517Combined sources
Helixi145 – 1539Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF5X-ray3.00A4-138[»]
1BP7X-ray3.00A/B/C/D2-153[»]
1G9YX-ray2.05A/B2-153[»]
1G9ZX-ray1.80A/B2-153[»]
1MOWX-ray2.40A/D/G/J17-163[»]
1N3EX-ray2.50A/B/G/H1-163[»]
1N3FX-ray2.00A/B/G/H1-163[»]
1T9IX-ray1.60A/B1-163[»]
1T9JX-ray2.00A/B1-163[»]
1U0CX-ray2.50A/B1-163[»]
1U0DX-ray2.90A/B1-163[»]
2I3PX-ray2.30A/B1-153[»]
2I3QX-ray2.30A/B1-153[»]
2O7MX-ray2.00A/B1-156[»]
2VBJX-ray1.95A/B2-153[»]
2VBLX-ray1.80A/B1-153[»]
2VBNX-ray1.90A/B1-153[»]
2VBOX-ray1.80A/B1-153[»]
4AABX-ray2.50A/B2-153[»]
4AADX-ray3.10A/B2-153[»]
4AAEX-ray2.60A/B2-154[»]
4AAFX-ray2.50A/B2-153[»]
4AAGX-ray2.80A/B2-153[»]
4AQUX-ray2.30A/B2-153[»]
4AQXX-ray2.20A/B2-153[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05725.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni26 – 3813Interaction with DNAAdd
BLAST
Regioni44 – 474Interaction with DNA
Regioni68 – 703Interaction with DNA
Regioni138 – 1436Interaction with DNA

Sequence similaritiesi

Belongs to the LAGLIDADG endonuclease family.Curated

Family and domain databases

Gene3Di3.10.28.10. 1 hit.
InterProiIPR027434. Homing_endonucl.
IPR004860. LAGLIDADG_2.
[Graphical view]
PfamiPF00961. LAGLIDADG_1. 1 hit.
[Graphical view]
SUPFAMiSSF55608. SSF55608. 1 hit.

Sequencei

Sequence statusi: Complete.

P05725-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNTKYNKEFL LYLAGFVDGD GSIIAQIKPN QSYKFKHQLS LTFQVTQKTQ
60 70 80 90 100
RRWFLDKLVD EIGVGYVRDR GSVSDYILSE IKPLHNFLTQ LQPFLKLKQK
110 120 130 140 150
QANLVLKIIE QLPSAKESPD KFLEVCTWVD QIAALNDSKT RKTTSETVRA
160
VLDSLSEKKK SSP
Length:163
Mass (Da):18,696
Last modified:July 27, 2011 - v2
Checksum:i22B625C0CD72F575
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01977 Genomic DNA. Translation: CAA26008.2.
PIRiA23091.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01977 Genomic DNA. Translation: CAA26008.2.
PIRiA23091.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AF5X-ray3.00A4-138[»]
1BP7X-ray3.00A/B/C/D2-153[»]
1G9YX-ray2.05A/B2-153[»]
1G9ZX-ray1.80A/B2-153[»]
1MOWX-ray2.40A/D/G/J17-163[»]
1N3EX-ray2.50A/B/G/H1-163[»]
1N3FX-ray2.00A/B/G/H1-163[»]
1T9IX-ray1.60A/B1-163[»]
1T9JX-ray2.00A/B1-163[»]
1U0CX-ray2.50A/B1-163[»]
1U0DX-ray2.90A/B1-163[»]
2I3PX-ray2.30A/B1-153[»]
2I3QX-ray2.30A/B1-153[»]
2O7MX-ray2.00A/B1-156[»]
2VBJX-ray1.95A/B2-153[»]
2VBLX-ray1.80A/B1-153[»]
2VBNX-ray1.90A/B1-153[»]
2VBOX-ray1.80A/B1-153[»]
4AABX-ray2.50A/B2-153[»]
4AADX-ray3.10A/B2-153[»]
4AAEX-ray2.60A/B2-154[»]
4AAFX-ray2.50A/B2-153[»]
4AAGX-ray2.80A/B2-153[»]
4AQUX-ray2.30A/B2-153[»]
4AQXX-ray2.20A/B2-153[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59771N.

Protein family/group databases

REBASEi2540. I-CreI.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP05725.

Family and domain databases

Gene3Di3.10.28.10. 1 hit.
InterProiIPR027434. Homing_endonucl.
IPR004860. LAGLIDADG_2.
[Graphical view]
PfamiPF00961. LAGLIDADG_1. 1 hit.
[Graphical view]
SUPFAMiSSF55608. SSF55608. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The chloroplast ribosomal intron of Chlamydomonas reinhardtii codes for a polypeptide related to mitochondrial maturases."
    Rochaix J.-D., Rahire M., Michel F.
    Nucleic Acids Res. 13:975-984(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Monnat R.J.
    Submitted (MAY-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 42; 110 AND 111.
  3. "Cleavage and recognition pattern of a double-strand-specific endonuclease (I-CreI) encoded by the chloroplast 23S rRNA intron of Chlamydomonas reinhardtii."
    Thompson A.J., Yuan X., Kudlicki W., Herin D.L.
    Gene 119:247-251(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  4. "Characterization of the cleavage site and the recognition sequence of the I-CreI DNA endonuclease encoded by the chloroplast ribosomal intron of Chlamydomonas reinhardtii."
    Duerrenberger F., Rochaix J.-D.
    Mol. Gen. Genet. 236:409-414(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  5. "The structure of I-CreI, a group I intron-encoded homing endonuclease."
    Heath P.J., Stephens K.M., Monnat R.J. Jr., Stoddard B.L.
    Nat. Struct. Biol. 4:468-476(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
  6. "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites."
    Chevalier B.S., Monnat R.J. Jr., Stoddard B.L.
    Nat. Struct. Biol. 8:312-316(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 2-153 IN COMPLEX WITH DIVALENT METAL CATIONS, COFACTOR, SUBUNIT.
  7. "Design, activity, and structure of a highly specific artificial endonuclease."
    Chevalier B.S., Kortemme T., Chadsey M.S., Baker D., Monnat R.J., Stoddard B.L.
    Mol. Cell 10:895-905(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 9-163 IN COMPLEX WITH DNA AND DIVALENT METAL CATIONS, SUBUNIT, MUTAGENESIS.
  8. "Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI."
    Chevalier B., Turmel M., Lemieux C., Monnat R.J. Jr., Stoddard B.L.
    J. Mol. Biol. 329:253-269(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL CATIONS, SUBUNIT, COFACTOR.
  9. "Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease."
    Chevalier B., Sussman D., Otis C., Noel A.-J., Turmel M., Lemieux C., Stephens K., Monnat R.J. Jr., Stoddard B.L.
    Biochemistry 43:14015-14026(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANTS ASN-20 AND GLU-47 IN COMPLEX WITH CALCIUM IONS AND DNA, COFACTOR, SUBUNIT, MUTAGENESIS OF ASP-20; GLN-47 AND LYS-98.
  10. "Isolation and characterization of new homing endonuclease specificities at individual target site positions."
    Sussman D., Chadsey M., Fauce S., Engel A., Bruett A., Monnat R. Jr., Stoddard B.L., Seligman L.M.
    J. Mol. Biol. 342:31-41(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH DNA, SUBUNIT, MUTAGENESIS OF GLN-26 AND TYR-33.
  11. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-153 IN COMPLEX WITH DNA, SUBUNIT, MUTAGENESIS OF TYR-33; GLN-44 AND ARG-68.
  12. "The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage."
    Prieto J., Redondo P., Padro D., Arnould S., Epinat J.-C., Paques F., Blanco F.J., Montoya G.
    Nucleic Acids Res. 35:3262-3271(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-156 IN COMPLEX WITH DNA, SUBUNIT, MUTAGENESIS OF SER-138; LYS-139; LYS-142 AND THR-143.

Entry informationi

Entry nameiDNE1_CHLRE
AccessioniPrimary (citable) accession number: P05725
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: July 27, 2011
Last modified: November 11, 2015
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.