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(-) Description

Title :  STRUCTURE OF THE COOPERATIVE EXCISIONASE (XIS)-DNA COMPLEX REVEALS A MICRONUCLEOPROTEIN FILAMENT
 
Authors :  M. A. Abbani, C. V. Papagiannis, M. D. Sam, D. Cascio, R. C. Johnson, R. T.
Date :  18 Sep 06  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Excisionase; Recombination Directionality Factor; Site Specific Recombination; Micronucleoprotein Filament, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Abbani, C. V. Papagiannis, M. D. Sam, D. Cascio, R. C. Johnson, R. T. Clubb
Structure Of The Cooperative Xis-Dna Complex Reveals A Micronucleoprotein Filament That Regulates Phage Lambda Intasome Assembly.
Proc. Natl. Acad. Sci. Usa V. 104 2109 2007
PubMed-ID: 17287355  |  Reference-DOI: 10.1073/PNAS.0607820104

(-) Compounds

Molecule 1 - 15-MER DNA
    Chains: D
    Engineered: YES
    Other Details: FIRST STRAND, 5'-END
    Synthetic: YES
 
Molecule 2 - 19-MER DNA
    Chains: E
    Engineered: YES
    Other Details: FIRST STRAND, 3'-END
    Synthetic: YES
 
Molecule 3 - 34-MER DNA
    Chains: F
    Engineered: YES
    Other Details: SECOND STRAND
    Synthetic: YES
 
Molecule 4 - EXCISIONASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSBET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: XIS
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid: 10710
    Synonym: XIS

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2IEF)

(-) Sites  (0, 0)

(no "Site" information available for 2IEF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IEF)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:31 -Pro A:32
2Phe B:31 -Pro B:32
3Phe C:31 -Pro C:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IEF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IEF)

(-) Exons   (0, 0)

(no "Exon" information available for 2IEF)

(-) 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:55
 aligned with VXIS_LAMBD | P03699 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:55
                                    10        20        30        40        50     
            VXIS_LAMBD    1 MYLTLQEWNARQRRPRSLETVRRWVRECRIFPPPVKDGREYLFHESAVKVDLNRP 55
               SCOP domains d2iefa_ A: Excisionase Xis                              SCOP domains
               CATH domains 2iefA00 A:1-55  [code=1.10.1660.20, no name defined]    CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhh....hhhhhhhhhhh..ee...eee..eeee....ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2ief A  1 MYLTLQEWNARQRRPRSLETVRRWVRESRIFPPPVKDGREYLFHESAVKVDLNRP 55
                                    10        20        30        40        50     


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with VXIS_LAMBD | P03699 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:54
                                    10        20        30        40        50    
            VXIS_LAMBD    1 MYLTLQEWNARQRRPRSLETVRRWVRECRIFPPPVKDGREYLFHESAVKVDLNR 54
               SCOP domains d2iefb_ B: Excisionase Xis                             SCOP domains
               CATH domains 2iefB00 B:1-54  [code=1.10.1660.20, no name defined]   CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhh.....hhhhhhhhhhh..ee...eee..eeeee...ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  2ief B  1 MYLTLQEWNARQRRPRSLETVRRWVRESRIFPPPVKDGREYLFHESAVKVDLNR 54
                                    10        20        30        40        50    


Chain C from PDB  Type:PROTEIN  Length:53
 aligned with VXIS_LAMBD | P03699 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:53
                                    10        20        30        40        50   
            VXIS_LAMBD    1 MYLTLQEWNARQRRPRSLETVRRWVRECRIFPPPVKDGREYLFHESAVKVDLN 53
               SCOP domains d2iefc_ C: Excisionase Xis                            SCOP domains
               CATH domains 2iefC00 C:1-53  [code=1.10.1660.20, no name defined]  CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhh......hhhhhhhhhhh..ee...eee..eeeee...ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2ief C  1 MYLTLQEWNARQRRPRSLETVRRWVRESRIFPPPVKDGREYLFHESAVKVDLN 53
                                    10        20        30        40        50   


Chain D from PDB  Type:DNA  Length:15
                                              
                  2ief D  1 ATATGTTGTGTTTTA 15
                                    10     


Chain E from PDB  Type:DNA  Length:19
                                                  
                  2ief E 16 CAGTATTATGTAGTCTGTT 34
                                    25         


Chain F from PDB  Type:DNA  Length:34
                                                                 
                  2ief F 35 TAACAGACTACATAATACTGTAAAACACAACATA 68
                                    44        54        64
   Legend:   → Mismatch (orange background)
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    → 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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IEF)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (VXIS_LAMBD | P03699)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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.

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  Cis Peptide Bonds
    Phe A:31 - Pro A:32   [ RasMol ]  
    Phe B:31 - Pro B:32   [ RasMol ]  
    Phe C:31 - Pro C:32   [ RasMol ]  
 

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  2ief
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  VXIS_LAMBD | P03699
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 Related Entries

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

UniProtKB/Swiss-Prot
        VXIS_LAMBD | P03699: 1lx8 1rh6 2og0 5j0n

(-) Related Entries Specified in the PDB File

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