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(-) Description

Title :  STRUCTURE OF THE ARM-TYPE BINDING DOMAIN OF HPI INTEGRASE
 
Authors :  A. Szwagierczak, U. Antonenka, G. M. Popowicz, T. Sitar, T. A. Holak, A.
Date :  14 Sep 09  (Deposition) - 06 Oct 09  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Four Stranded Beta-Sheet, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Szwagierczak, U. Antonenka, G. M. Popowicz, T. Sitar, T. A. Holak, A. Rakin
Structures Of The Arm-Type Binding Domains Of Hpi And Hai7 Integrases
J. Biol. Chem. V. 284 31664 2009
PubMed-ID: 19737930  |  Reference-DOI: 10.1074/JBC.M109.059261

(-) Compounds

Molecule 1 - INTEGRASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ARM-TYPE BINDING DOMAIN, UNP RESIDUES 1-80
    Gene: INT, INT2
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: CP4-LIKE INTEGRASE, INT PROTEIN, PUTATIVE PROPHAGE INTEGRASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:14 , LYS A:16 , PHE A:18 , VAL A:30 , LYS A:31 , PRO A:32BINDING SITE FOR RESIDUE NA A 89

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:56 -Pro A:57
2Leu A:77 -Asn A:78

 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:77
 aligned with Q9Z3B4_YERPE | Q9Z3B4 from UniProtKB/TrEMBL  Length:420

    Alignment length:77
                                    11        21        31        41        51        61        71       
          Q9Z3B4_YERPE    2 SLTDAKIRTLKPSDKPFKVSDSHGLYLLVKPGGSRHWYLKYRISGKESRIALGAYPAISLSDARQQREGIRKMLALN 78
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains -DUF4102-3jtzA01 A:3-78                                                       Pfam domains
         Sec.struct. author ..hhhhhhhh......eeee....eeeee.....eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  3jtz A  2 SLTDAKIRTLKPSDKPFKVSDSHGLYLLVKPGGSRHWYLKYRISGKESRIALGAYPAISLSDARQQREGIRKMLALN 78
                                    11        21        31        41        51        61        71
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3JTZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF4102] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9Z3B4_YERPE | Q9Z3B4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008979    prophage integrase activity    Catalysis of the integration of prophage DNA into a target DNA molecule, usually a bacterial chromosome, via a sequence-specific recombination event which involves the formation of an intasome, a DNA-protein-complex designed for site-specific recombination of the phage and host DNA.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0032359    provirus excision    The molecular events that lead to the excision of a viral genome from the host genome.

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        Q9Z3B4_YERPE | Q9Z3B4: 3rmp

(-) Related Entries Specified in the PDB File

3ju0