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(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MN
 
Authors :  R. Molina, M. J. Marcaida, P. Redondo, M. Marenchino, M. D'Abramo, G. Mo J. Prieto
Date :  02 Mar 15  (Deposition) - 17 Jun 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,J,K,L,N
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  J,K,L,N  (1x)
Biol. Unit 3:  E,F,G,H  (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
    ChainsA, E, J
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System VectorPET24D
    Expression System Vector TypePLASMID
    Organism ScientificDESULFUROCOCCUS MOBILIS
    Organism Taxid2274
 
Molecule 2 - 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
    ChainsB, F, K
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
    ChainsC, G, L
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - 25MER
    ChainsD, H, N
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHJKLN
Biological Unit 1 (1x)ABCD        
Biological Unit 2 (1x)        JKLN
Biological Unit 3 (1x)    EFGH    

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MN6Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDT G:16 , DT G:17 , DC H:11 , DT H:12BINDING SITE FOR RESIDUE ACT G1026
2AC2SOFTWAREASP A:21 , ALA A:116 , DA B:14 , DC D:16BINDING SITE FOR RESIDUE MN A1188
3AC3SOFTWAREGLY A:20 , GLU A:117 , HOH A:2004 , DG C:15 , DC D:15BINDING SITE FOR RESIDUE MN A1189
4AC4SOFTWAREASP E:21 , ALA E:116 , HOH E:2033 , HOH E:2034 , DA F:14 , DC H:16BINDING SITE FOR RESIDUE MN E1188
5AC5SOFTWAREGLY E:20 , GLU E:117 , HOH E:2005 , DG G:15 , DC H:15BINDING SITE FOR RESIDUE MN E1189
6AC6SOFTWAREASP J:21 , ALA J:116 , HOH J:2059 , DA K:14 , DC N:16BINDING SITE FOR RESIDUE MN J1187
7AC7SOFTWAREGLY J:20 , GLU J:117 , HOH J:2003 , DG L:15 , DC N:15BINDING SITE FOR RESIDUE MN J1188

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AK9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:30 -Gly A:31
2Lys E:30 -Gly E:31
3Lys J:30 -Gly J:31
4His J:181 -Leu J:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AK9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AK9)

(-) Exons   (0, 0)

(no "Exon" information available for 5AK9)

(-) 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 hhhhhhhhhhhhhhhhheeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ak9 A   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 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
                                              
                 5ak9 B   1 GCCTTGCCGGGTAA  14
                                    10    

Chain C from PDB  Type:DNA  Length:11
                                           
                 5ak9 C  15 GTTCCGGCGCG  25
                                    24 

Chain D from PDB  Type:DNA  Length:25
                                                         
                 5ak9 D   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    10        20     

Chain E from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ak9 E   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPP 187
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   

Chain F from PDB  Type:DNA  Length:14
                                              
                 5ak9 F   1 GCCTTGCCGGGTAA  14
                                    10    

Chain G from PDB  Type:DNA  Length:11
                                           
                 5ak9 G  15 GTTCCGGCGCG  25
                                    24 

Chain H from PDB  Type:DNA  Length:25
                                                         
                 5ak9 H   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    10        20     

Chain J from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhheeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh...eeeeeee....eeeeee...hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ak9 J   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLP 186
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184  

Chain K from PDB  Type:DNA  Length:14
                                              
                 5ak9 K   1 GCCTTGCCGGGTAA  14
                                    10    

Chain L from PDB  Type:DNA  Length:11
                                           
                 5ak9 L  15 GTTCCGGCGCG  25
                                    24 

Chain N from PDB  Type:DNA  Length:25
                                                         
                 5ak9 N   1 CGCGCCGGAACTTACCCGGCAAGGC  25
                                    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 5AK9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AK9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AK9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DMO1_DESMO | P215051b24 1mow 2vs7 2vs8 4d6n 4d6o 4un7 4un8 4un9 4una 4unb 4unc 4ut0 5a0w 5akf 5akm 5akn

(-) Related Entries Specified in the PDB File

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
5akm THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG
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