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(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN
 
Authors :  J. Prieto, P. Redondo, N. Merino, M. Villate, F. J. Blanco, R. Molina
Date :  21 Apr 15  (Deposition) - 04 May 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,H,I,J,K,L
Biol. Unit 1:  A,C,D,K,L  (1x)
Biol. Unit 2:  B,E,H,I,J  (1x)
Keywords :  Hydrolase-Dna Complex, Gene Targeting, Genetics, Protein-Dna Interaction, Homing Endonucleases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Prieto, P. Redondo, N. Merino, M. Villate, G. Montoya, F. J. Blanco, R. Molina
Structure Of The I-Scei Nuclease Complexed With Its Dsdna Target And Three Catalytic Metal Ions.
Acta Crystallogr. , Sect. F V. 72 473 2016
PubMed-ID: 27303901  |  Reference-DOI: 10.1107/S2053230X16007512

(-) Compounds

Molecule 1 - INTRON-ENCODED ENDONUCLEASE I-SCEI
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: PET24D
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Gene: SCEI, OMEGA, SECY, Q0160
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA
 
Molecule 2 - INTRON-ENCODED ENDONUCLEASE I-SCEI
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: PET24D
    Expression System Taxid: 469008
    Gene: SCEI, OMEGA, SECY, Q0160
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: 21S RRNA INTRON MATURASE, HOMING ENDONUCLEASE OMEGA
 
Molecule 3 - 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
    Chains: C, E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
    Chains: D, H
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
    Chains: I, L
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 6 - 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
    Chains: J, K
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEHIJKL
Biological Unit 1 (1x): A CD    KL
Biological Unit 2 (1x):  B  EHIJ  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MN8Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:344 , ASP A:445 , DA C:14 , DT D:16 , DC K:15 , DC L:17BINDING SITE FOR RESIDUE MN A1527
2AC2SOFTWARELEU A:342 , GLY A:343 , ASP A:445 , DC K:15BINDING SITE FOR RESIDUE MN A1528
3AC3SOFTWAREASP A:344 , ASP A:444 , DA C:14 , DC L:17BINDING SITE FOR RESIDUE MN A1529
4AC4SOFTWAREDT D:16 , DC K:15BINDING SITE FOR RESIDUE MN D1017
5AC5SOFTWAREDA H:15 , DT H:16 , DC J:15BINDING SITE FOR RESIDUE MN H1017
6AC6SOFTWAREGLY B:343 , ASP B:445 , DC J:15BINDING SITE FOR RESIDUE MN B1529
7AC7SOFTWAREASP B:344 , ASP B:444 , ASP B:445 , DA E:14 , DT H:16 , DC I:17 , DC J:15BINDING SITE FOR RESIDUE MN B1530
8AC8SOFTWAREASP B:344 , ASP B:444 , DA E:14 , DC I:17BINDING SITE FOR RESIDUE MN B1531

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0M)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhh..........eeee.....eeeeeeee......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhheee...........eee.....hhhhhhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhh...hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0m A 303 NIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNKSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLPN 526
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522    


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.....hhhhhhhh......hhhhhhhhhhhhhh..eee........eeeeee.hhhhhhhhhhhhhhhh....eeeeee.....eeeeeeee......hhhhhhhhh.........hhhhhh.hhhhhhhhhhhheee...........eee.....hhhhhhhhhhhhhhh....eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0m B 302 KNIKKNQVMNLGPNSKLLKEYKSQLIELNIEQFEAGIGLILGDAYIRSRDEGKTYCMQFEWKNKAYMDHVCLLYDQWVLSPPHKKERVNHLGNLVITWGAQTFKHQAFNKLANLFIVNNKKTIPNNLVENYLTPMSLAYWFMDDGGKWDYNKNSTNTSIVLNTQSFTFEEVEYLVKGLRNKFQLNCYVKINKNKPIIYIDSMSYLIFYNLIKPYLIPQMMYKLPNTI 528
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       


Chain C from PDB  Type:DNA  Length:13
                                             
                 5a0m C   2 ACGCTAGGGATAA  14
                                    11   


Chain D from PDB  Type:DNA  Length:15
                                               
                 5a0m D   2 GTATTACCCTGTTAT  16
                                    11     


Chain E from PDB  Type:DNA  Length:14
                                              
                 5a0m E   1 CACGCTAGGGATAA  14
                                    10    


Chain H from PDB  Type:DNA  Length:15
                                               
                 5a0m H   2 GTATTACCCTGTTAT  16
                                    11     


Chain I from PDB  Type:DNA  Length:9
                                         
                 5a0m I  17 CCCTAGCGT  25


Chain J from PDB  Type:DNA  Length:11
                                           
                 5a0m J  15 CAGGGTAATAC  25
                                    24 


Chain K from PDB  Type:DNA  Length:11
                                           
                 5a0m K  15 CAGGGTAATAC  25
                                    24 


Chain L from PDB  Type:DNA  Length:9
                                         
                 5a0m L  17 CCCTAGCGT  25
   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  (0, 0)

(no "SCOP Domain" information available for 5A0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A0M)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        SCE1_YEAST | P03882: 1r7m 3c0w 3c0x 3ool 3oor

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