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(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG
 
Authors :  R. Molina, M. J. Marcaida, P. Redondo, M. Marenchino, M. D'Abramo, G. Mo J. Prieto
Date :  04 Mar 15  (Deposition) - 17 Jun 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Biol. Unit 1:  F,G,H,I,J  (1x)
Biol. Unit 2:  K,L,M,N,O  (1x)
Biol. Unit 3:  A,B,C,D,E  (1x)
Keywords :  Hydrolase, Gene Targeting, Genetics, Protein-Dna Interaction, Homing Endonucleases, X-Ray Crystallography. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Molina, M. J. Marcaida, P. Redondo, M. Marenchino, P. Duchateau, M. D'Abramo, G. Montoya, J. Prieto
Engineering A Nickase On The Homing Endonuclease I-Dmoi Scaffold.
J. Biol. Chem. V. 290 18534 2015
PubMed-ID: 26045557  |  Reference-DOI: 10.1074/JBC.M115.658666

(-) Compounds

Molecule 1 - HOMING ENDONUCLEASE I-DMOI
    Chains: A, F, K
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PET24D
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: DESULFUROCOCCUS MOBILIS
    Organism Taxid: 2274
 
Molecule 2 - 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
    Chains: B, G, L
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
    Chains: C, H, M
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
    Chains: D, I, N
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 5 - 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
    Chains: E, J, O
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112131415
Asymmetric Unit : ABCDEFGHIJKLMNO
Biological Unit 1 (1x):      FGHIJ     
Biological Unit 2 (1x):           KLMNO
Biological Unit 3 (1x): ABCDE          

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:111 , ASN A:183 , HOH A:2020BINDING SITE FOR RESIDUE ACT A1188
2AC2SOFTWAREARG A:99 , ASN A:131BINDING SITE FOR RESIDUE ACT A1189
3AC3SOFTWARETYR F:114 , LYS F:120BINDING SITE FOR RESIDUE ACT F1180
4AC4SOFTWAREASP F:21 , ALA F:116 , HOH F:2003 , DA G:14 , DC J:16BINDING SITE FOR RESIDUE MG F1181
5AC5SOFTWARESER F:20 , GLU F:117 , HOH F:2001 , DG H:15 , DC I:15BINDING SITE FOR RESIDUE MG F1182
6AC6SOFTWAREASP A:21 , ALA A:116 , GLU A:117 , HOH A:2002 , DA B:14 , DC D:15 , DC E:16BINDING SITE FOR RESIDUE MG A1190
7AC7SOFTWAREASP K:21 , ALA K:116 , HOH K:2003 , DA L:14 , DC N:15 , DC O:16BINDING SITE FOR RESIDUE MG K1182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:31 -Asn A:32
2Gly F:31 -Asn F:32
3Lys K:30 -Gly K:31
4Gly K:31 -Asn K:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AKM)

(-) 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:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhh.hhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5akm A   5 ENVSGISAYLLGLIISDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 187
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   


Chain B from PDB  Type:DNA  Length:14
                                              
                 5akm B   1 GCCTTGCCGGGTAA  14
                                    10    


Chain C from PDB  Type:DNA  Length:11
                                           
                 5akm C  15 GTTCCGGCGCG  25
                                    24 


Chain D from PDB  Type:DNA  Length:15
                                               
                 5akm D   1 CGCGCCGGAACTTAC  15
                                    10     


Chain E from PDB  Type:DNA  Length:10
                                          
                 5akm E  16 CCGGCAAGGC  25
                                    25


Chain F from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5akm F   6 NVSGISAYLLGLIISDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILS 179
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    


Chain G from PDB  Type:DNA  Length:14
                                              
                 5akm G   1 GCCTTGCCGGGTAA  14
                                    10    


Chain H from PDB  Type:DNA  Length:11
                                           
                 5akm H  15 GTTCCGGCGCG  25
                                    24 


Chain I from PDB  Type:DNA  Length:15
                                               
                 5akm I   1 CGCGCCGGAACTTAC  15
                                    10     


Chain J from PDB  Type:DNA  Length:10
                                          
                 5akm J  16 CCGGCAAGGC  25
                                    25


Chain K from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5akm K   4 NENVSGISAYLLGLIISDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSH 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain L from PDB  Type:DNA  Length:14
                                              
                 5akm L   1 GCCTTGCCGGGTAA  14
                                    10    


Chain M from PDB  Type:DNA  Length:11
                                           
                 5akm M  15 GTTCCGGCGCG  25
                                    24 


Chain N from PDB  Type:DNA  Length:15
                                               
                 5akm N   1 CGCGCCGGAACTTAC  15
                                    10     


Chain O from PDB  Type:DNA  Length:10
                                          
                 5akm O  16 CCGGCAAGGC  25
                                    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 5AKM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMO1_DESMO | P21505: 1b24 1mow 2vs7 2vs8 4d6n 4d6o 4un7 4un8 4un9 4una 4unb 4unc 4ut0 5a0w 5ak9 5akf 5akn

(-) Related Entries Specified in the PDB File

5ak9 THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MN
5akf THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE CODING STRAND A AND IN THE PRESENCE OF 2MM MN
5akn THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE NON-CODING STRAND B AND IN THE PRESENCE OF 2MM MN