2CRX | PD0103 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION

Authors :   D. N. Gopaul, F. Guo, G. D. Vanduyne

Date :   19 Jun 98 (Deposition) - 14 Dec 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (2x)

Keywords :   Cre Recombinase, Holliday Junction, Recombination, Recombinase/Dna Complex, Hydrolase, Ligase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. N. Gopaul, F. Guo, G. D. Van Duyne
Structure Of The Holliday Junction Intermediate In Cre-Loxp Site-Specific Recombination.
Embo J. V. 17 4175 1998
PubMed-ID: 9670032 | Reference-DOI: 10.1093/EMBOJ/17.14.4175
(for further references see the PDB file header)

Molecule 1 - DNA 35-MER
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (CRE RECOMBINASE)
	Atcc	:	25404-B1
	Chains	:	A, B
	Collection	:	25404-B1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ENTEROBACTERIA PHAGE P1
	Organism Taxid	:	10678
	Synonym	:	CRE-HJ2, RGBPP1 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 2CRX)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	CIA	UNKNOWN	ARG A:173 , HIS A:289 , ARG A:292 , TRP A:315 , TYR A:324	RECOMBINASE ACTIVE SITE.
2	CIB	UNKNOWN	ARG B:173 , HIS B:289 , ARG B:292 , TRP B:315 , TYR B:324	RECOMBINASE ACTIVE SITE.

(no "SS Bond" information available for 2CRX)

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 2CRX)

(no "PROSITE Motif" information available for 2CRX)

(no "Exon" information available for 2CRX)

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:305
 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 d2crxa1 A:19-129 Cre recombinase                                                                               d2crxa2 A:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -2crxA02 A:20-130  [code=1.10.150.130, no name defined]                                                         -2crxA01 A:132-331 Intergrase catalytic core                                                                                                                                                             ---------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhh.....eeeee..eeee...-----------.....hhhhhhhhhhhh..............eee...eee........hhhhhhhhhhhhhhhh..-------.......hhhhhhhhhhhh....hhhhhhhh....hhhhhhhh........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2crx A  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIG-----------EKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGA-------YLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLDSETGAMVRLLED 341
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         - |     218       228       238       248       258       268      |  -    |  288       298       308       318       328       338   
                                                                                                                                                                                                             198         210                                                              275     283

Chain B from PDB  Type:PROTEIN  Length:309
 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 d2crxb1 B:19-129 Cre recombinase                                                                               d2crxb2 B:130-341 Cre recombinase                                                                                                                                                                                    SCOP domains
               CATH domains -2crxB02 B:20-130  [code=1.10.150.130, no name defined]                                                         -2crxB01 B:132-333 Intergrase catalytic core                                                                                                                                                               -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhh.hhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhh..hhheee.....eeeee.--------..eeee..hhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhh................hhhhhhhhhhhh....hhhhhhhh....hhhhhh...------.hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2crx B  19 TSDEVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLMENSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIG--------AGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIR------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       | -    |  338   
                                                                                                                                                                                                             198      207                                                                                                                    326    333

Chain C from PDB  Type:DNA  Length:35
                                                                   
                 2crx C   1 TATAACTTCGTATAGCATATGCTATACGAAGTTAT  35
                                    10        20        30

Chain D from PDB  Type:DNA  Length:34
                                                                  
                 2crx D   2 ATAACTTCGTATAGCATATGCTATACGAAGTTAT  35
                                    11        21        31

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(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

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	2crxA02	A:20-130
1b	2crxB02	B:20-130

Topology: hpI Integrase; Chain A (31)

Homologous Superfamily: Intergrase catalytic core (31)

[unclassified] (26)

2a	2crxB01	B:132-333
2b	2crxA01	A:132-331

(no "Pfam Domain" information available for 2CRX)

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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	Sites
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		CIB	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:64 - Pro A:65	[ RasMol ]
		Phe B:64 - Pro B:65	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

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Cis Peptide Bonds (2, 2)

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