Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  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
 
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) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
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 I 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 LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26)
    Synthetic: YES
 
Molecule 2 - 34-MER
    Chains: D
    Engineered: YES
    Other Details: BOTTOM STRAND OF LOXM7 ENGINEERED DNA SUBSTRATE (LOXP(C7/G28,T8/A27,A9/T26)
    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: CRE SITE-SPECIFIC RECOMBINASE MUTANT (I174A, T258L, R259S, E262H, 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 1PVP)

(-) Sites  (0, 0)

(no "Site" information available for 1PVP)

(-) SS Bonds  (0, 0)

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

(-) 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 1PVP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PVP)

(-) 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:323
 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 d1pvpa1 A:19-129 Cre recombinase                                                                               d1pvpa2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -1pvpA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -1pvpA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhh.............ee...............ee.hhhhhhhhhhhhhhhhhhhh.......ee.....ee.......hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhh......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvp A  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRAAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSLSALHGIFGATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 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   


Chain B from PDB  Type:PROTEIN  Length:318
 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 d1pvpb1 B:19-129 Cre recombinase                                                                               d1pvpb2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -1pvpB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -1pvpB01 B:132-314 Intergrase catalytic core                                                                                                                                            --------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1pvpB01 B:138-326                                                                                                                                                            --------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------Phage_integrase-1pvpB02 B:138-326                                                                                                                                                            --------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhh..hhh.eee.....eeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.......ee.....ee.......hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhh..-----.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvp B  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRAAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSLSALHGIFGATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIR-----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       | -   |   338   
                                                                                                                                                                                                                                                                                                                                             326   332         


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


Chain D from PDB  Type:DNA  Length:34
                                                                  
                 1pvp D   1 ATAACTCTATATAGCATACATTATATAGAGTTAT  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. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pvp)
 
  Sites
(no "Sites" information available for 1pvp)
 
  Cis Peptide Bonds
    Phe A:64 - Pro A:65   [ RasMol ]  
    Phe B:64 - Pro B:65   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pvp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RECR_BPP1 | P06956
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RECR_BPP1 | P06956
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RECR_BPP1 | P06956: 1crx 1drg 1f44 1kbu 1ma7 1nzb 1ouq 1pvq 1pvr 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
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
1pvr 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
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