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(-) Description

Title :  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
 
Authors :  R. Molina, M. J. Marcaida, P. Redondo, M. Marenchino, M. D'Abramo, G. Mo J. Prieto
Date :  03 Mar 15  (Deposition) - 17 Jun 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  I,J,K,L  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Hydrolase, Gene Targeting, Genetics, Protein-Dna Interaction, Homing Endonucleases (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, I
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA PLYSS
    Expression System VectorPET24D
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificDESULFUROCOCCUS MOBILIS
    Organism Taxid2274
    SynonymI-DMOI
 
Molecule 2 - 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
    ChainsC, G, K
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
    ChainsB, F, J
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - 25MER
    ChainsD, H, L
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)        IJKL
Biological Unit 2 (1x)    EFGH    
Biological Unit 3 (1x)ABCD        

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
3MN3Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:182 , ASN A:183BINDING SITE FOR RESIDUE ACT A1184
2AC2SOFTWAREDG B:6 , DA D:22BINDING SITE FOR RESIDUE CL B1015
3AC3SOFTWAREASN I:131BINDING SITE FOR RESIDUE CL I1181
4AC4SOFTWAREASP A:21 , ALA A:116 , HOH A:2007 , HOH A:2055 , DA B:14 , DC D:16BINDING SITE FOR RESIDUE MN A1185
5AC5SOFTWAREASP E:21 , ALA E:116 , HOH E:2046 , DA F:14 , DC H:16BINDING SITE FOR RESIDUE MN E1182
6AC6SOFTWAREASP I:21 , ALA I:116 , DA J:14 , DC L:16BINDING SITE FOR RESIDUE MN I1180

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:30 -Gly A:31
2Leu A:182 -Asn A:183
3Lys E:30 -Gly E:31
4Lys I:30 -Gly I:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AKF)

(-) 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:179
                                                                                                                                                                                                                   
               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
                 5akf A   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLN 183
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174         

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

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

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

Chain E from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               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
                 5akf E   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILSS 180
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      

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

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

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

Chain I from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               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
                 5akf I   5 ENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITAKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYELRVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDMTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGVYVLNISLRDRIKFVHTILS 179
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     

Chain J from PDB  Type:DNA  Length:14
                                              
                 5akf J   1 GCCTTGCCGGGTAA  14
                                    10    

Chain K from PDB  Type:DNA  Length:11
                                           
                 5akf K  15 GTTCCGGCGCG  25
                                    24 

Chain L from PDB  Type:DNA  Length:25
                                                         
                 5akf L   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 5AKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5ak9 5akm 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
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