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(-) Description

Title :  ARCHAEAL INTRON-ENCODED HOMING ENDONUCLEASE I-VDI141I COMPLEXED WITH DNA
 
Authors :  N. Nomura, Y. Nomura, D. Sussman, B. L. Stoddard
Date :  13 Aug 08  (Deposition) - 30 Dec 08  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Dna Complex, Laglidadg, Homing, Endonuclease, Dna Recognition, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nomura, Y. Nomura, D. Sussman, D. Klein, B. L. Stoddard
Recognition Of A Common Rdna Target Site In Archaea And Eukarya By Analogous Laglidadg And His-Cys Box Homing Endonucleases
Nucleic Acids Res. V. 36 6988 2008
PubMed-ID: 18984620  |  Reference-DOI: 10.1093/NAR/GKN846

(-) Compounds

Molecule 1 - RRNA INTRON-ENCODED ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVDII65M/I107M-10
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 23S RRNA INTRON (VDI141.L1927)
    Mutation: YES
    Organism Scientific: VULCANISAETA DISTRIBUTA
    Organism Taxid: 164451
    Strain: IC-141
    Synonym: HOMING ENDONUCLEASE I-VDI141I
 
Molecule 2 - DNA (5'- D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')
    Chains: C
    Engineered: YES
    Other Details: I-VDI141I DNA TARGET SITE
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')
    Chains: D
    Engineered: YES
    Other Details: I-VDI141I DNA TARGET SITE
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')
    Chains: E
    Engineered: YES
    Other Details: I-VDI141I DNA TARGET SITE
    Synthetic: YES
 
Molecule 5 - DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')
    Chains: F
    Engineered: YES
    Other Details: I-VDI141I DNA TARGET SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EOH3Ligand/IonETHANOL
2MG5Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , ALA B:218 , DG D:503 , EOH D:801 , DA E:613BINDING SITE FOR RESIDUE MG A 702
2AC2SOFTWAREASP A:39 , DA C:493BINDING SITE FOR RESIDUE MG A 704
3AC3SOFTWAREGLU A:19 , GLU B:219 , DA C:502 , DG D:503 , DA E:613 , DG F:614BINDING SITE FOR RESIDUE MG B 701
4AC4SOFTWAREASP B:239 , DG E:604BINDING SITE FOR RESIDUE MG B 705
5AC5SOFTWAREALA A:18 , GLU B:219 , GLN B:246 , DA C:502 , DG F:614BINDING SITE FOR RESIDUE MG C 703
6AC6SOFTWAREMG A:702 , LYS B:301 , DG D:503 , DA E:612BINDING SITE FOR RESIDUE EOH D 801
7AC7SOFTWAREDT C:500 , DT E:611BINDING SITE FOR RESIDUE EOH E 803
8AC8SOFTWARELYS A:101 , DG F:614BINDING SITE FOR RESIDUE EOH F 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E54)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E54)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E54)

(-) Exons   (0, 0)

(no "Exon" information available for 3E54)

(-) 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:159
 aligned with Q6L703_9CREN | Q6L703 from UniProtKB/TrEMBL  Length:169

    Alignment length:159
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         
         Q6L703_9CREN     4 EEDFKEGYILGFIEAEGSFSVSIKFQRDVFGGVRLDPVFSITQKNREVLEAIKEHLGIGRIIEKAGQPNTYVYVVDNFNELVKLINFLNKYADFMIVKKRQFLIFREIANGLVNGEHLHINGLKRLVKLAYELTKESEKGYRKYDLNHVLSIIDKWDLG 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhheeeeeeeee...hhh.eeeeeeeeeee.hhhhhhhhhhhhh..eeee.......eeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e54 A   4 EEDFKEGYILGFIEAEGSFSVSIKFQRDVFGGVRLDPVFSITQKNREVLEAIKEHLGIGRIMEKAGQPNTYVYVVDNFNELVKLINFLNKYADFMIVKKRQFLMFREIANGLVNGEHLHINGLKRLVKLAYELTKESEKGYRKYDLNHVLSIIDKWDLG 162
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q6L703_9CREN | Q6L703 from UniProtKB/TrEMBL  Length:169

    Alignment length:159
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         
         Q6L703_9CREN     4 EEDFKEGYILGFIEAEGSFSVSIKFQRDVFGGVRLDPVFSITQKNREVLEAIKEHLGIGRIIEKAGQPNTYVYVVDNFNELVKLINFLNKYADFMIVKKRQFLIFREIANGLVNGEHLHINGLKRLVKLAYELTKESEKGYRKYDLNHVLSIIDKWDLG 162
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhheeeeeeee....hhhhheeeeeeeeee.hhhhhhhhhhhhh..eeee.......eeeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e54 B 204 EEDFKEGYILGFIEAEGSFSVSIKFQRDVFGGVRLDPVFSITQKNREVLEAIKEHLGIGRIMEKAGQPNTYVYVVDNFNELVKLINFLNKYADFMIVKKRQFLMFREIANGLVNGEHLHINGLKRLVKLAYELTKESEKGYRKYDLNHVLSIIDKWDLG 362
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         


Chain C from PDB  Type:DNA  Length:13
                                             
                 3e54 C 490 CTGACTCTCTTAA 502
                                   499   


Chain D from PDB  Type:DNA  Length:9
                                         
                 3e54 D 503 GGTAGCCAA 511


Chain E from PDB  Type:DNA  Length:13
                                             
                 3e54 E 601 TTGGCTACCTTAA 613
                                   610   


Chain F from PDB  Type:DNA  Length:9
                                         
                 3e54 F 614 GAGAGTCAG 622
   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 3E54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E54)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E54)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6L703_9CREN | Q6L703)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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  3e54
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  Q6L703_9CREN | Q6L703
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