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(-) Description

Title :  CRYSTAL STRUCTURE OF MMSOI/DNA COMPLEX WITH CALCIUM
 
Authors :  H. Li, R. J. Monnat
Date :  24 Nov 08  (Deposition) - 30 Jun 09  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Chloroplast, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, S. Pellenz, U. Ulge, B. L. Stoddard, R. J. Monnat
Generation Of Single-Chain Laglidadg Homing Endonucleases From Native Homodimeric Precursor Proteins.
Nucleic Acids Res. V. 37 1650 2009
PubMed-ID: 19153140  |  Reference-DOI: 10.1093/NAR/GKP004

(-) Compounds

Molecule 1 - SITE-SPECIFIC DNA ENDONUCLEASE I-MSOI
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET SYSTEM
    Expression System Strain: C2566
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ORF170, THE CHLOROPLAST LARGE SUBUNIT RDNA INTRON GENE
    Organism Scientific: MONOMASTIX SP. (STRAIN OKE-1), MONOMASTIX SP. OKE-1, UNIDENTIFIED
    Organism Taxid: 141716
    Other Details: FUSION PROTEIN COMPRISES RESIDUES 1-170 OF I-MSOI, A LINKER OF 33 RESIDUES (TGSGSGSKHPTLTLPTTTSQENLPNGSGSGSGT) AND A 2ND I-MSOI (1-170 RESIDUES).
    Strain: OKE-1
 
Molecule 2 - 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3'
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: THE PHYSIOLOGICAL DNA TARGET SITE OF I-MSOI IN THE CHLOROPLAST LARGE SUBUNIT RDNA OF MONOMASTIX
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *TP*TP*CP*TP*GP*C)-3'
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: THE PHYSIOLOGICAL DNA TARGET SITE OF I-MSOI IN THE CHLOROPLAST LARGE SUBUNIT RDNA OF MONOMASTIX
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:21 , ASP A:225 , HOH A:386 , HOH A:394 , DG B:515 , DC C:564BINDING SITE FOR RESIDUE CA A 374
2AC2SOFTWAREASP A:22 , GLY A:224 , HOH A:383 , HOH A:395 , DA B:514 , DG C:565BINDING SITE FOR RESIDUE CA A 375

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FD2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:168 -Ser A:169
2Thr A:171 -Gly A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FD2)

(-) Exons   (0, 0)

(no "Exon" information available for 3FD2)

(-) Sequences/Alignments

Asymmetric/Biological 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:338
 aligned with C0JWR6_MONSK | C0JWR6 from UniProtKB/TrEMBL  Length:170

    Alignment length:338
                                                                                                                                                                                               170                                                                                                                                                                            
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     |   -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -        
         C0JWR6_MONSK     5 NTLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKIESSP----------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fd2A01 A:5-178 Homing endonucleases                                                                                                                                          3fd2A02 A:207-370 Homing endonucleases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhh....eee......eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...................hhhhhhhhhhhhhhheeeeeeeee........eeeeeeeeeeee..hhhhhhhhhhhh....eee......eeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fd2 A   5 NTLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKIESSPTGSGSGSKKNTLQPTEAAYIAGFLDGDGSIYAKLIPRPDYKDIKYQVSLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIIGSTHLSIILPDLVPYLRIKKKQANRILHIINLYPQAQKNPSKFLDLVKIVDDVQNLNKRADELKSTNYDRLLEEFLKAGKIE 370
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   ||  212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        
                                                                                                                                                                                                       178|                                                                                                                                                                   
                                                                                                                                                                                                        207                                                                                                                                                                   


Chain B from PDB  Type:DNA  Length:24
                                                        
                 3fd2 B 501 GCAGAACGTCGTGAGACAGTTCCG 524
                                   510       520    


Chain C from PDB  Type:DNA  Length:24
                                                        
                 3fd2 C 551 CGGAACTGTCTCACGACGTTCTGC 574
                                   560       570
   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 3FD2)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FD2)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C0JWR6_MONSK | C0JWR6)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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  3fd2
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  3.1.-.-
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 Related Entries

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

UniProtKB/TrEMBL
        C0JWR6_MONSK | C0JWR6: 1m5x 2fld 3ko2

(-) Related Entries Specified in the PDB File

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