1KBU | PD0271 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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)

Molecule 1 - LOXP
	Chains	:	C
	Engineered	:	YES
	Other Details	:	PART OF HOLLIDAY JUNCTION
	Synthetic	:	YES

Molecule 2 - LOXP
	Chains	:	D
	Engineered	:	YES
	Other Details	:	PART OF HOLLIDAY JUNCTION
	Synthetic	:	YES

Molecule 3 - CRE RECOMBINASE
	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
	Organism Scientific	:	ENTEROBACTERIA PHAGE P1
	Organism Taxid	:	10678
	Other Details	:	LYS86 AND LYS201 INTERACTIONS WITH THE SCISSILE BASE SUGGEST HOW STRAND EXCHANGE ORDER IS DETERMINED
	Synonym	:	CRE SITE-SPECIFIC RECOMBINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1KBU)

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 1KBU)

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.130, no name defined] (26)

[unclassified] (23)

1a	1kbuA02	A:20-130
1b	1kbuB02	B:20-130

Topology: hpI Integrase; Chain A (31)

Homologous Superfamily: Intergrase catalytic core (31)

[unclassified] (26)

2a	1kbuA01	A:132-331
2b	1kbuB01	B:132-333

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DNA-mend (28)

Family: Phage_integrase (15)

Enterobacteria phage P1 (Bacteriophage P1) (11)

1a	Phage_integrase-1kbuB01	B:138-328
1b	Phage_integrase-1kbuB02	B:138-328

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	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 ]

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	1kbu
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	RECR_BPP1 \| P06956
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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.

Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (2, 2)

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SCOP Domains (2, 4)

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Pfam Domains (1, 2)

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