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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE CRE RECOMBINASE-LOXP SYNAPSE
 
Authors :  E. Ennifar, J. E. W. Meyer, F. Buchholz, A. F. Stewart, D. Suck
Date :  17 Feb 03  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Cre, Recombinase, Dna, Replication/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ennifar, J. E. W. Meyer, F. Buchholz, A. F. Stewart, D. Suck
Crystal Structure Of A Wild-Type Cre Recombinase-Loxp Synapse Reveals A Novel Spacer Conformation Suggesting An Alternative Mechanism For Dna Cleavage Activation
Nucleic Acids Res. V. 31 5449 2003
PubMed-ID: 12954782  |  Reference-DOI: 10.1093/NAR/GKG732
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOXP DNA
    Chains: C, G
    Engineered: YES
    Other Details: FIRST STRAND OF LOXP SITE
    Synthetic: YES
 
Molecule 2 - LOXP DNA
    Chains: D, H
    Engineered: YES
    Other Details: SECOND STRAND OF LOXP SITE
    Synthetic: YES
 
Molecule 3 - CRE RECOMBINASE
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEM
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synonym: GST-LOXP-CRE RECOMBINASE FUSION PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1IOD2Ligand/IonIODIDE ION
2MG10Ligand/IonMAGNESIUM ION
3UMP2Mod. Nucleotide2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:40 , DT C:125BINDING SITE FOR RESIDUE MG A 5301
2AC2SOFTWAREHIS A:269BINDING SITE FOR RESIDUE MG A 5302
3AC3SOFTWAREGLN A:156 , ARG A:159 , ASN A:160 , DC D:106BINDING SITE FOR RESIDUE MG D 5304
4AC4SOFTWAREDT D:107BINDING SITE FOR RESIDUE MG D 5305
5AC5SOFTWAREDG G:117BINDING SITE FOR RESIDUE MG G 5306
6AC6SOFTWAREDG C:117BINDING SITE FOR RESIDUE MG C 5308
7AC7SOFTWARETHR F:87 , HIS F:91 , DA G:112BINDING SITE FOR RESIDUE MG F 5309
8AC8SOFTWAREDA D:105BINDING SITE FOR RESIDUE MG D 5310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:64 -Pro A:65
2Phe B:64 -Pro B:65
3Phe E:64 -Pro E:65
4Phe F:64 -Pro F:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NZB)

(-) 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:332
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:332
                                    19        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    10 NLPALPVDATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1nzba1 A:10-129 Cre recombinase                                                                                        d1nzba2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains ----------1nzbA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -1nzbA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.eeee...eeeee.............eee.hhhhhhhhhhhhhhhh...........ee.....ee.......hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzb A  10 NLPALPVDATSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    19        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 d1nzbb1 B:20-129 Cre recombinase                                                                              d1nzbb2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains 1nzbB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -1nzbB01 B:132-330 Intergrase catalytic core                                                                                                                                                            ----------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhh........eeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh........ee...ee........hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhh....................hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzb 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:37
                                                                     
                 1nzb C 100 CGATAACuTCGTATAATGTATGCTATACGAAGTTATC 136
                                   109       119       129       
                                 107-UMP                         


Chain D from PDB  Type:DNA  Length:37
                                                                     
                 1nzb D 100 GGATAACTTCGTATAGCATACATTATACGAAGTTATC 136
                                   109       119       129       


Chain E from PDB  Type:PROTEIN  Length:321
 aligned with RECR_BPP1 | P06956 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:321
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
            RECR_BPP1    21 DEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
               SCOP domains d1nzbe1 E:21-129 Cre recombinase                                                                             d1nzbe2 E:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains 1nzbE02 E:21-130  [code=1.10.150.130, no name defined]                                                        -1nzbE01 E:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhh..............eee.............eee.hhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhh.......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzb E  21 DEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 


Chain F 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 d1nzbf1 F:20-129 Cre recombinase                                                                              d1nzbf2 F:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains 1nzbF02 F:20-130  [code=1.10.150.130, no name defined]                                                         -1nzbF01 F:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------Phage_integrase-1nzbF01 F:138-331                                                                                                                                                                 ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------Phage_integrase-1nzbF02 F:138-331                                                                                                                                                                 ---------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------Phage_integrase-1nzbF03 F:138-331                                                                                                                                                                 ---------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------Phage_integrase-1nzbF04 F:138-331                                                                                                                                                                 ---------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.eee.....eeeeeeee..eeeeeeeeee...hhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhh.........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzb F  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 G from PDB  Type:DNA  Length:37
                                                                     
                 1nzb G 100 CGATAACuTCGTATAATGTATGCTATACGAAGTTATC 136
                                   109       119       129       
                                 107-UMP                         


Chain H from PDB  Type:DNA  Length:37
                                                                     
                 1nzb H 100 GGATAACTTCGTATAGCATACATTATACGAAGTTATC 136
                                   109       119       129
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,E,F   (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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  1nzb
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  RECR_BPP1 | P06956
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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 1ouq 1pvp 1pvq 1pvr 1q3u 1q3v 1xns 1xo0 2crx 2hof 2hoi 3c28 3c29 3crx 3mgv 4crx 5crx

(-) Related Entries Specified in the PDB File

1ouq COVALENT INTERMEDIATE (LOW RESOLUTION)
1q3u PRE-CLEAVAGE COMPLEX (HIGH RESOLUTION)
1q3v COVALENT INTERMEDIATE (HIGH RESOLUTION)