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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THAP DOMAIN FROM D. MELANOGASTER P-ELEMENT TRANSPOSASE IN COMPLEX WITH ITS NATURAL DNA BINDING SITE
 
Authors :  A. Sabogal, A. Y. Lyubimov, J. M. Berger, D. C. Rio
Date :  22 Oct 09  (Deposition) - 08 Dec 09  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Thap Domain, Dna-Binding Domain, Zinc-Finger, Beta-Alpha-Beta, P- Element Transposase, Dna Integration, Dna Recombination, Dna- Binding, Metal-Binding, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sabogal, A. Y. Lyubimov, J. E. Corn, J. M. Berger, D. C. Rio
Thap Proteins Target Specific Dna Sites Through Bipartite Recognition Of Adjacent Major And Minor Grooves.
Nat. Struct. Mol. Biol. V. 17 117 2010
PubMed-ID: 20010837  |  Reference-DOI: 10.1038/NSMB.1742

(-) Compounds

Molecule 1 - 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3'
    Chains: A
    Engineered: YES
    Other Details: 5'-GTTAAG(BRDU)GGA-3'
    Other Details - Source: SYNTHETIC BROMINATED SSDNA OLIGO
    Synthetic: YES
 
Molecule 2 - 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3'
    Chains: B
    Engineered: YES
    Other Details: 5'-(BRDU)CCACTTAAC-3'
    Other Details - Source: SYNTHETIC BROMINATED SSDNA OLIGO
    Synthetic: YES
 
Molecule 3 - TRANSPOSABLE ELEMENT P TRANSPOSASE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: T
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: P-ELEMENT TRANSPOSASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:4 , CYS C:7 , CYS C:44 , HIS C:47BINDING SITE FOR RESIDUE ZN C 78

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_THAPPS50950 Zinc finger THAP-type profilePELET_DROME1-77  1C:1-77

(-) Exons   (0, 0)

(no "Exon" information available for 3KDE)

(-) 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:DNA  Length:10
                                         
                  3kde A  1 GTTAAGuGGA 10
                                  | 10
                                  7-BRU


Chain B from PDB  Type:DNA  Length:10
                                         
                  3kde B 11 uCCACTTAAC 20
                            |       20
                            |         
                           11-BRU     


Chain C from PDB  Type:PROTEIN  Length:75
 aligned with PELET_DROME | Q7M3K2 from UniProtKB/Swiss-Prot  Length:751

    Alignment length:77
                                    10        20        30        40        50        60        70       
           PELET_DROME    1 MKYCKFCCKAVTGVKLIHVPKCAIKRKLWEQSLGCSLGENSQICDTHFNDSQWKAAPAKGQTFKRRRLNADAVPSKV 77
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains THAP-3kdeC01 C:1-77                                                           Pfam domains
         Sec.struct. author ..ee....ee.....eee...hhhhhhhhhhhhh.......eee.hhhhhhhh...--................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_THAP  PDB: C:1-77 UniProt: 1-77                                            PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  3kde C  1 MKYCKFCCKAVTGVKLIHVPKCAIKRKLWEQSLGCSLGENSQICDTHFNDSQWKAA--KGQTFKRRRLNADAVPSKV 77
                                    10        20        30        40        50     |  60        70       
                                                                                  56 59
   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 3KDE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: THAP] (3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (PELET_DROME | Q7M3K2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003693    P-element binding    Interacting selectively and non-covalently with any P-element, a class of Drosophila transposon responsible for hybrid dysgenesis.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004803    transposase activity    Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006313    transposition, DNA-mediated    Any process involved in a type of transpositional recombination which occurs via a DNA intermediate.

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