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(-) Description

Title :  CRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I
 
Authors :  F. Guo, D. N. Gopaul, G. D. Van Duyne
Date :  02 Jul 97  (Deposition) - 14 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Site-Specific Recombinase, Protein:Dna Complex, Reaction Intermediate, Complex (Recombinase/Dna), Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Guo, D. N. Gopaul, G. D. Van Duyne
Structure Of Cre Recombinase Complexed With Dna In A Site-Specific Recombination Synapse.
Nature V. 389 40 1997
PubMed-ID: 9288963  |  Reference-DOI: 10.1038/37925
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T) -3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - CRE RECOMBINASE
    Atcc: 25404-B1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: CRE
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:173 , HIS B:289 , ARG B:292 , TRP B:315 , TYR B:324 , DG C:15BINDING SITE FOR RESIDUE PO4 B 342
2ACTUNKNOWNARG A:173 , HIS A:289 , ARG A:292 , TRP A:315 , TYR A:324NULL
3ACUUNKNOWNARG B:173 , HIS B:289 , ARG B:292 , TRP B:315 , TYR B:324NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 1CRX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CRX)

(-) 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:322
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:322
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
            RECR_BPP1    20 SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1crxa1 A:20-129 Cre recombinase                                                                              d1crxa2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains 1crxA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -1crxA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhh.hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhh..hhheee.hhh.eeeee...........eeee..hhhhhhhhhhhh...hhh........ee.....ee........hhhhhhhhhhhhhhhh................hhhhhhhhhhhh....hhhhhhhh.......hhhh....hhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1crx A  20 SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain B from PDB  Type:PROTEIN  Length:322
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:322
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
            RECR_BPP1    20 SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1crxb1 B:20-129 Cre recombinase                                                                              d1crxb2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains 1crxB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -1crxB01 B:132-333 Intergrase catalytic core                                                                                                                                                               -------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhh.hhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhh....hhheee.....eeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhh.hhh........ee.....ee........hhhhhhhhhhhhhhhh................hhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhh.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1crx B  20 SDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain C from PDB  Type:DNA  Length:15
                                               
                 1crx C   1 TATAACTTCGTATAG  15
                                    10     


Chain D from PDB  Type:DNA  Length:19
                                                   
                 1crx D   1 ATATGCTATACGAAGTTAT  19
                                    10         


Chain E from PDB  Type:DNA  Length:15
                                               
                 1crx E   2 ATAACTTCGTATAGC  16
                                    11     


Chain F from PDB  Type:DNA  Length:19
                                                   
                 1crx F   1 ATATGCTATACGAAGTTAT  19
                                    10
   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/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CRX)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological 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. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RECR_BPP1 | P06956: 1drg 1f44 1kbu 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

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