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(-) Description

Title :  BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE LOXP (WILDTYPE) RECOGNITION SITE
 
Authors :  E. P. Baldwin, S. S. Martin, J. Abel, K. A. Gelato, H. Kim, P. G. Schultz, S. W. Santoro
Date :  28 Jun 03  (Deposition) - 17 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Cre, Recombinase, Dna, Cre-Loxp Recombination, Recombination/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. P. Baldwin, S. S. Martin, J. Abel, K. A. Gelato, H. Kim, P. G. Schultz, S. W. Santoro
A Specificity Switch In Selected Cre Recombinase Variants Is Mediated By Macromolecular Plasticity And Water.
Chem. Biol. V. 10 1085 2003
PubMed-ID: 14652076  |  Reference-DOI: 10.1016/J.CHEMBIOL.2003.10.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 34-MER
    Chains: C
    Engineered: YES
    Other Details: TOP STRAND OF LOXP WILDTYPE DNA SUBSTRATE
    Synthetic: YES
 
Molecule 2 - 34-MER
    Chains: D
    Engineered: YES
    Other Details: BOTTOM STRAND OF LOXP WILDTYPE DNA SUBSTRATE
    Synthetic: YES
 
Molecule 3 - RECOMBINASE CRE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B(+)
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CRE
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Other Details: SELECTED CRE SITE-SPECIFIC RECOMBINASE MUTANT (I174L,T258N, R259S, E262G, E266G)

 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 1PVR)

(-) Sites  (0, 0)

(no "Site" information available for 1PVR)

(-) SS Bonds  (0, 0)

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

(-) 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 1PVR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PVR)

(-) 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 d1pvra1 A:18-129 Cre recombinase                                                                                d1pvra2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains --1pvrA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -1pvrA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhh......eee.....eeee.............eee.hhhhhhhhhhhhhhhh...........ee.....ee.......hhhhhhhhhhhhhhhhhh..hhhhh.......hhhhhhhhhhhhhh..hhhhhh.......hhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pvr A  18 ATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRLAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSNSALGGIFGATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 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:320
 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 d1pvrb1 B:19-129 Cre recombinase                                                                               d1pvrb2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -1pvrB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -1pvrB01 B:132-314 Intergrase catalytic core                                                                                                                                            --------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1pvrB01 B:138-328                                                                                                                                                              ------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1pvrB02 B:138-328                                                                                                                                                              ------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.eee.....eeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.......ee.....ee.......hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhh....---.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvr B  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRLAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSNSALGGIFGATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNL---TGAMVRLLED 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   
                                                                                                                                                                                                                                                                                                                                               328 332         


Chain C from PDB  Type:DNA  Length:33
                                                                 
                 1pvr C   1 ATAACTTCGTATAATGATGCTATACGAAGTTAT  34
                                    10     || 21        31   
                                          16|                
                                           18                


Chain D from PDB  Type:DNA  Length:34
                                                                  
                 1pvr D   1 ATAACTTCGTATAGCATACATTATACGAAGTTAT  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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        RECR_BPP1 | P06956: 1crx 1drg 1f44 1kbu 1ma7 1nzb 1ouq 1pvp 1pvq 1q3u 1q3v 1xns 1xo0 2crx 2hof 2hoi 3c28 3c29 3crx 3mgv 4crx 5crx

(-) Related Entries Specified in the PDB File

1crx CRYSTAL STRUCTURE OF A COVALENT CRE-SUICIDE SUBSTRATE DNA COMPLEX
1f44 CRYSTAL STRUCTURE OF A TRIMERIC CRE-LOX SYNAPSE
1kbu CRYSTAL STRUCTURE OF A CRE-LOXP HOLLIDAY JUNCTION COMPLEX
1ma7 CRYSTAL STRUCTURE OF CRE-LOXP(A8/T27) HOLLIDAY JUNCTION COMPLEX
1nzb CRYSTAL STRUCTURE OF A CRE-LOXP PRECLEAVAGE COMPLEX
1ouq CRYSTAL STRUCTURE OF A CRE-LOXP COVALENT COMPLEX
1pvp BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, ALSHG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7
1pvq BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7
3crx CRYSTAL STRUCTURE OF CRE COMPLEXED WITH AN IMMOBILIZED DNA HOLLIDAY JUNCTION
4crx CRYSTAL STRUCTURE OF AN UNCLEAVED COMPLEX OF CRE BOUND TO LOXS, A SYMMETRIZED LOX SEQUENCE