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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL LAGLIDADG HOMING ENDONUCLEASE, I-ONUI (FROM OPHIOSTOMA NOVO-ULMI SUBSP. AMERICANA)
 
Authors :  R. Takeuchi, B. L. Stoddard
Date :  16 Feb 11  (Deposition) - 20 Jul 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Comlex, Laglidadg Family, Hydrolase, Dna Binding, Mitochondrion, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Takeuchi, A. R. Lambert, A. N. Mak, K. Jacoby, R. J. Dickson, G. B. Gloor, A. M. Scharenberg, D. R. Edgell, B. L. Stoddard
Tapping Natural Reservoirs Of Homing Endonucleases For Targeted Gene Modification.
Proc. Natl. Acad. Sci. Usa V. 108 13077 2011
PubMed-ID: 21784983  |  Reference-DOI: 10.1073/PNAS.1107719108

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN 3/HOMING ENDONUCLEASE-LIKE PROTEIN FUSION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 413-715
    Gene: RPS3/HEG FUSION
    Organism Scientific: OPHIOSTOMA NOVO-ULMI SUBSP. AMERICANA
    Organism Taxid: 170178
 
Molecule 2 - DNA (26-MER)
    Chains: B
    Engineered: YES
    Other Details: TARGET DNA SEQUENCE (TOP STRAND)
    Other Details - Source: TARGET SEQUENCE FOR THE CO-CRYSTALLIZED PROTEIN
    Synthetic: YES
 
Molecule 3 - DNA (26-MER)
    Chains: C
    Engineered: YES
    Other Details: TARGET DNA SEQUENCE (BOTTOM STRAND)
    Other Details - Source: TARGET SEQUENCE FOR THE CO-CRYSTALLIZED PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:21 , GLU A:22 , GLU A:178 , DC B:14 , DA B:15 , DT C:15 , DA C:16BINDING SITE FOR RESIDUE MG A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QQY)

(-) 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:299
 aligned with Q4VWW5_OPHNO | Q4VWW5 from UniProtKB/TrEMBL  Length:715

    Alignment length:302
                                   423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713  
         Q4VWW5_OPHNO   414 AYMSRRESINPWILTGFADAEGSFLLRIRNNNKSSVGYSTELGFQITLHNKDKSILENIQSTWKVGVIANSGDNAVSLKVTRFEDLKVIIDHFEKYPLITQKLGDYMLFKQAFCVMENKEHLKINGIKELVRIKAKLNWGLTDELKKAFPEIISKERSLINKNIPNFKWLAGFTSGEGCFFVNLIKSKSKLGVQVQLVFSITQHIKDKNLMNSLITYLGCGYIKEKNKSEFSWLDFVVTKFSDINDKIIPVFQENTLIGVKLEDFEDWCKVAKLIEEKKHLTESGLDEIKKIKLNMNKGRVF 715
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.eeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeee....eeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.....---........hhhhhhhhhhhheeeeeeeee......eeeeeeeeeeehhhhhhhhhhhhhhhh..eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qqy A   2 AYMSRRESINPWILTGFADAEGSFLLRIRNNNKSSVGYSTELGFQITLHNKDKSILENIQSTWKVGVIANSGDNAVSLKVTRFEDLKVIIDHFEKYPLITQKLGDYMLFKQAFCVMENKEHLKINGIKELVRIKAKLNWGLTDELKKAFPEIIS---SLINKNIPNFKWLAGFTSGEGCFFVNLIKSKSKLGVQVQLVFSITQHIKDKNLMNSLITYLGCGYIKEKNKSEFSWLDFVVTKFSDINDKIIPVFQENTLIGVKLEDFEDWCKVAKLIEEKKHLTESGLDEIKKIKLNMNKGRVF 303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   |   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  
                                                                                                                                                                                   155 159                                                                                                                                                


Chain B from PDB  Type:DNA  Length:26
                                                          
                 3qqy B   1 CTTTCCACTTATTCAACCTTTTACCC  26
                                    10        20      


Chain C from PDB  Type:DNA  Length:26
                                                          
                 3qqy C   1 GGTAAAAGGTTGAATAAGTGGAAAGG  26
                                    10        20
   Legend:   → Mismatch (orange background)
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  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 3QQY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4VWW5_OPHNO | Q4VWW5)
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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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