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(-) Description

Title :  THE HOMING ENDONUCLEASE I-SCEI BOUND TO ITS DNA RECOGNITION REGION
 
Authors :  C. M. Moure, F. S. Gimble, F. A. Quiocho
Date :  21 Oct 03  (Deposition) - 26 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Protein-Dna Complex, Endonuclease, Laglidadg, Beta-Saddle, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Moure, F. S. Gimble, F. A. Quiocho
The Crystal Structure Of The Gene Targeting Homing Endonuclease I-Scei Reveals The Origins Of Its Target Site Specificity
J. Mol. Biol. V. 334 685 2003
PubMed-ID: 14636596  |  Reference-DOI: 10.1016/J.JMB.2003.09.068
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP *TP*AP*AP*TP*AP*C)-3'
    Chains: C, E
    Engineered: YES
    Other Details: DNA-TOP STRAND
    Synthetic: YES
 
Molecule 2 - 5'- D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP*AP*TP*CP*CP*CP *TP*AP*GP*CP*GP*T)-3'
    Chains: D, F
    Engineered: YES
    Other Details: DNA-BOTTOM STRAND
    Synthetic: YES
 
Molecule 3 - INTRON-ENCODED ENDONUCLEASE I-SCEI
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSCM525
    Expression System Strain: ER2267
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SECY
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:85 , ASP B:344 , ASP B:444 , DA E:14 , DC F:17 , HOH F:27BINDING SITE FOR RESIDUE CA B 536
2AC2SOFTWAREDC E:15 , HOH E:310 , HOH E:311 , DA F:15 , DT F:16 , HOH F:30 , HOH F:35BINDING SITE FOR RESIDUE CA E 302
3AC3SOFTWAREHOH B:141 , GLY B:343 , ASP B:344 , ASP B:445 , DC E:15 , DC F:17BINDING SITE FOR RESIDUE CA B 537
4AC4SOFTWAREASP A:44 , ASP A:144 , DA C:14 , DC D:17 , HOH D:30BINDING SITE FOR RESIDUE CA A 304
5AC5SOFTWAREDC C:15 , HOH C:315 , DA D:15 , DT D:16 , HOH D:31 , HOH D:41 , HOH D:47BINDING SITE FOR RESIDUE CA C 305
6AC6SOFTWAREGLY A:43 , ASP A:44 , ASP A:145 , HOH A:327 , DC C:15 , DC D:17BINDING SITE FOR RESIDUE CA A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R7M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R7M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R7M)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1Q01601Q0160.1Mito:61022-61729708SCE1_YEAST1-2352352A:3-225
B:303-525		223
223

(-) Sequences/Alignments

Asymmetric 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 d1r7ma1 A:3-120 DNA endonuclease I-SceI                                                                               d1r7ma2 A:121-225 DNA endonuclease I-SceI                                                                 SCOP domains
               CATH domains 1r7mA01 A:3-122 Homing endonucleases                                                                                    1r7mA02 A:123-225 Homing endonucleases                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee...hhhhhhhhhhhee..ee....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
                 1r7m 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 B 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 d1r7mb1 B:303-420 DNA endonuclease I-SceI                                                                             d1r7mb2 B:421-525 DNA endonuclease I-SceI                                                                 SCOP domains
               CATH domains 1r7mB01 B:303-422 Homing endonucleases                                                                                  1r7mB02 B:423-525 Homing endonucleases                                                                  CATH domains
           Pfam domains (1) ------------------------------LAGLIDADG_2-1r7mB01 B:333-509                                                                                                                                                    ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------LAGLIDADG_2-1r7mB02 B:333-509                                                                                                                                                    ---------------- Pfam domains (2)
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhheee...........eee.....hhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:303-525 UniProt: 1-235 [INCOMPLETE]                                                                                                                                                                            Transcript 1
                 1r7m B 303 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLP 525
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522   


Chain C from PDB  Type:DNA  Length:24
                                                        
                 1r7m C   2 ACGCTAGGGATAACAGGGTAATAC  25
                                    11        21    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 1r7m D   2 GTATTACCCTGTTATCCCTAGCGT  25
                                    11        21    


Chain E from PDB  Type:DNA  Length:24
                                                        
                 1r7m E   2 ACGCTAGGGATAACAGGGTAATAC  25
                                    11        21    


Chain F from PDB  Type:DNA  Length:24
                                                        
                 1r7m F   2 GTATTACCCTGTTATCCCTAGCGT  25
                                    11        21
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Homing_endonuc (19)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  1r7m
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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