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(-) Description

Title :  CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION
 
Authors :  S. S. Martin, E. Pulido, V. C. Chu, T. Lechner, E. P. Baldwin
Date :  06 Nov 01  (Deposition) - 07 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Site-Specific Recombinase, Holliday Junction Complex, Dna- Protein Co-Crystal, Int Recombinase Mechanism, Hydrolase, Ligase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Martin, E. Pulido, V. C. Chu, T. S. Lechner, E. P. Baldwin
The Order Of Strand Exchanges In Cre-Loxp Recombination And Its Basis Suggested By The Crystal Structure Of A Cre-Loxp Holliday Junction Complex
J. Mol. Biol. V. 319 107 2002
PubMed-ID: 12051940  |  Reference-DOI: 10.1016/S0022-2836(02)00246-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOXP
    ChainsC
    EngineeredYES
    Other DetailsPART OF HOLLIDAY JUNCTION
    SyntheticYES
 
Molecule 2 - LOXP
    ChainsD
    EngineeredYES
    Other DetailsPART OF HOLLIDAY JUNCTION
    SyntheticYES
 
Molecule 3 - CRE RECOMBINASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCRE
    Organism ScientificENTEROBACTERIA PHAGE P1
    Organism Taxid10678
    Other DetailsLYS86 AND LYS201 INTERACTIONS WITH THE SCISSILE BASE SUGGEST HOW STRAND EXCHANGE ORDER IS DETERMINED
    SynonymCRE SITE-SPECIFIC RECOMBINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1KBU)

(-) Sites  (0, 0)

(no "Site" information available for 1KBU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KBU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:64 -Pro A:65
2Phe B:64 -Pro B:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KBU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KBU)

(-) Exons   (0, 0)

(no "Exon" information available for 1KBU)

(-) Sequences/Alignments

Asymmetric 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:324
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:324
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    
            RECR_BPP1    18 ATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1kbua1 A:18-129 Cre recombinase                                                                                d1kbua2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains --1kbuA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -1kbuA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhh.eee.............eee...hhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh...hhhhhh.......hhhhhhh.......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kbu A  18 ATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:323
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338   
            RECR_BPP1    19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1kbub1 B:19-129 Cre recombinase                                                                               d1kbub2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -1kbuB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -1kbuB01 B:132-333 Intergrase catalytic core                                                                                                                                                               -------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1kbuB01 B:138-328                                                                                                                                                              ------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1kbuB02 B:138-328                                                                                                                                                              ------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhh.hhh.eee.....eeeee...........eeee.hhhhhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhh....----.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kbu B  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNL----GAMVRLLED 341
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    |  338   
                                                                                                                                                                                                                                                                                                                                               328  333        

Chain C from PDB  Type:DNA  Length:34
                                                                  
                 1kbu C   1 ATAAGTTCGTATAATGTATGCTATACGAAGTTAT  34
                                    10        20        30    

Chain D from PDB  Type:DNA  Length:34
                                                                  
                 1kbu D   1 ATAACTTCGTATAGCATACATTATACGAACTTAT  34
                                    10        20        30    

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DNA-mend (28)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RECR_BPP1 | P06956)
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: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. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

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    Phe A:64 - Pro A:65   [ RasMol ]  
    Phe B:64 - Pro B:65   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        RECR_BPP1 | P069561crx 1drg 1f44 1ma7 1nzb 1ouq 1pvp 1pvq 1pvr 1q3u 1q3v 1xns 1xo0 2crx 2hof 2hoi 3c28 3c29 3crx 3mgv 4crx 5crx

(-) Related Entries Specified in the PDB File

1crx 1CRX IS CRE/LOX COVALENT INTERMEDIATE.
1drg 1DRG IS CRE TRIMER/LOX Y-JUNCTION COMPLEX.
1f44 1F44 IS CRE TRIMER/LOX Y-JUNCTION COMPLEX.
2crx 2CRX IS CRE RECOMBINASE-HOLLIDAY JUNCTION COMPLEX.
3crx 3CRX IS CRE RECOMBINASE-HOLLIDAY JUNCTION COMPLEX.
4crx 4CRX IS CRE/LOX PRECLEAVAGE COMPLEX.