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(-) Description

Title :  CRYSTAL STRUCTURE OF LAGLIDADG MEGANUCLEASE I-CPAMI BOUND TO UNCLEAVED DNA
 
Authors :  J. P. Hallinan, B. K. Kaiser, B. L. Stoddard
Date :  02 Mar 15  (Deposition) - 23 Mar 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Hydrolase-Dna Complex, Laglidadg, Homing Endonuclease, Meganuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Lambert, J. P. Hallinan, B. W. Shen, J. K. Chik, J. M. Bolduc, N. Kulshina, L. I. Robins, B. K. Kaiser, J. Jarjour, K. Havens, A. M. Scharenberg, B. L. Stoddard
Indirect Dna Sequence Recognition And Its Impact On Nucleas Cleavage Activity.
Structure V. 24 862 2016
PubMed-ID: 27133026  |  Reference-DOI: 10.1016/J.STR.2016.03.024

(-) Compounds

Molecule 1 - MEGANUCLEASE I-CPAMI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 122-416
    Gene: MTSRRNA I4
    Organism Common: CHESNUT BLIGHT FUNGUS
    Organism Scientific: CRYPHONECTRIA PARASITICA
    Organism Taxid: 5116
 
Molecule 2 - DNA (28-MER)
    Chains: E, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (28-MER)
    Chains: F, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:17 , ASP A:177 , HOH A:401 , HOH A:406 , HOH E:204 , DT F:17binding site for residue CA A 301
02AC2SOFTWAREGLU A:18 , GLY A:176 , ASP A:177 , HOH A:401 , DT E:16 , DT F:17 , HOH F:201binding site for residue CA A 302
03AC3SOFTWAREPHE A:6 , ASN A:7 , ARG A:55 , GLN A:259binding site for residue EDO A 303
04AC4SOFTWAREALA B:17 , ASP B:177 , DT D:17binding site for residue CA B 301
05AC5SOFTWAREGLU B:18 , GLY B:176 , ASP B:177 , DT C:16 , DT D:16 , DT D:17binding site for residue CA B 302
06AC6SOFTWAREASN A:268 , GLU A:271 , ASN B:268 , GLU B:271binding site for residue CA B 303
07AC7SOFTWAREVAL B:196 , GLN B:197 , LEU B:198 , VAL B:240 , DT D:5 , DG D:6binding site for residue EDO B 304
08AC8SOFTWARESER A:179 , ARG A:236 , GLU A:238 , DA E:17binding site for residue EDO E 101
09AC9SOFTWAREDC E:8binding site for residue EDO F 101
10AD1SOFTWAREDT C:16 , DA D:13binding site for residue EDO D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YIS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YIS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YIS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YIS)

(-) Exons   (0, 0)

(no "Exon" information available for 4YIS)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhh............hhhhhhhhhhhhheeeeeee.........eeeeeeeeeee..hhhhhhhhhhhh..hhhhh.eee...eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yis A   5 SFNPWFLTGFSDAECSFSILIQANSKYSTGWRIKPVFAIGLHKKDNELLKRIQSYLGVGKIHIHGKDSIQFRIDSPKELEVIINHFENYPLVTAKQADYTLFKKALDVIKNKEHLSQKGLLKLVGIKASLNLGLNGSLKEAFPNWEELQIDRPSYVNKGIPDPNWISGFASGDSSFNVKISNSPTSLLNKRVQLRFGIGLNIREKALIQYLVAYFDLSDNLKNIYFDLNSARFEVVKFSDITDKIIPFFDKYSIQGKKSQDYQNFKEVADIIKSKNHLTSEGFQEILDIKASMNK 299
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     


Chain B from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.hhhhhh............hhhhhhhhhhhhheeeeeee.........eeeeeeeeeee..hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yis B   5 SFNPWFLTGFSDAECSFSILIQANSKYSTGWRIKPVFAIGLHKKDNELLKRIQSYLGVGKIHIHGKDSIQFRIDSPKELEVIINHFENYPLVTAKQADYTLFKKALDVIKNKEHLSQKGLLKLVGIKASLNLGLNGSLKEAFPNWEELQIDRPSYVNKGIPDPNWISGFASGDSSFNVKISNSPTSLLNKRVQLRFGIGLNIREKALIQYLVAYFDLNSARFEVVKFSDITDKIIPFFDKYSIQGKKSQDYQNFKEVADIIKSKNHLTSEGFQEILDIKASMNK 299
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      |235       245       255       265       275       285       295    
                                                                                                                                                                                                                                                  221|                                                                  
                                                                                                                                                                                                                                                   233                                                                  


Chain C from PDB  Type:DNA  Length:28
                                                            
                 4yis C   1 CCTAGCCCACAATATTAAGGCCATCCCC  28
                                    10        20        


Chain D from PDB  Type:DNA  Length:28
                                                            
                 4yis D   1 GGGATGGCCTTAATATTGTGGGCTAGGT  28
                                    10        20        


Chain E from PDB  Type:DNA  Length:28
                                                            
                 4yis E   1 CCTAGCCCACAATATTAAGGCCATCCCC  28
                                    10        20        


Chain F from PDB  Type:DNA  Length:28
                                                            
                 4yis F   1 GGGATGGCCTTAATATTGTGGGCTAGGT  28
                                    10        20
   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 4YIS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YIS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YIS)

(-) Gene Ontology  (3, 3)

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