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(-) Description

Title :  I-SCEI COMPLEXED WITH C/G+4 DNA SUBSTRATE
 
Authors :  R. Joshi, J-H. Chen, B. L. Golden, F. S. Gimble
Date :  31 Aug 10  (Deposition) - 17 Nov 10  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Homing Endonuclease, Intron Homing, Laglidadg, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Joshi, K. K. Ho, K. Tenney, J. H. Chen, B. L. Golden, F. S. Gimble
Evolution Of I-Scei Homing Endonucleases With Increased Dna Recognition Site Specificity.
J. Mol. Biol. V. 405 185 2011
PubMed-ID: 21029741  |  Reference-DOI: 10.1016/J.JMB.2010.10.029

(-) Compounds

Molecule 1 - INTRON ENCODED ENDONUCLEASE I-SCEI
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SCEI,OMEGA
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA
 
Molecule 2 - 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP *GP*TP*AP*AP*TP*AP*C)-3'
    Chains: C
    Engineered: YES
    Other Details: TOP STRAND OF I-SCEI C/G+4 DNA TARGET
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP *CP*TP*AP*GP*CP*GP*T)-3'
    Chains: D
    Engineered: YES
    Other Details: BOTTOM STRAND OF I-SCEI C/G+4 DNA TARGET
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , ASP A:144 , HOH A:243 , DA C:14 , DC D:17BINDING SITE FOR RESIDUE CA A 236
2AC2SOFTWAREGLY A:43 , ASP A:44 , ASP A:145 , HOH A:253 , DC C:15 , HOH D:31BINDING SITE FOR RESIDUE CA A 237
3AC3SOFTWAREDC C:15 , HOH C:31 , HOH C:33 , DT D:16 , HOH D:29BINDING SITE FOR RESIDUE CA C 26

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OOL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OOL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OOL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OOL)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1Q01601Q0160.1Mito:61022-61729708SCE1_YEAST1-2352351A:3-225223

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:223
 aligned with SCE1_YEAST | P03882 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           SCE1_YEAST     3 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLP 225
               SCOP domains d3oola1 A:3-120 automated matches                                                                                     d3oola2 A:121-225 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------LAGLIDADG_2-3oolA01 A:33-209                                                                                                                                                     ---------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhheee...........eee.....hhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-225 UniProt: 1-235 [INCOMPLETE]                                                                                                                                                                              Transcript 1
                 3ool A   3 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLP 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   


Chain C from PDB  Type:DNA  Length:24
                                                        
                 3ool C   2 ACGCTAGGGATAACCGGGTAATAC  25
                                    11        21    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 3ool D   2 GTATTACCCGGTTATCCCTAGCGT  25
                                    11        21
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OOL)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SCE1_YEAST | P03882)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SCE1_YEAST | P03882: 1r7m 3c0w 3c0x 3oor 5a0m

(-) Related Entries Specified in the PDB File

3oor