1GDT | PDE0115 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA-DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE

Authors :   W. Yang, T. A. Steitz

Date :   11 Apr 95 (Deposition) - 03 Apr 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Protein-Dna Complex, Double Helix, Overhanging Base, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Yang, T. A. Steitz
Crystal Structure Of The Site-Specific Recombinase Gamma Delta Resolvase Complexed With A 34 Bp Cleavage Site.
Cell(Cambridge, Mass. ) V. 82 193 1995
PubMed-ID: 7628011 | Reference-DOI: 10.1016/0092-8674(95)90307-0
(for further references see the PDB file header)

Molecule 1 - SITE I OF RES DNA
	Chains	:	C
	Engineered	:	YES
	Synonym	:	CROSSOVER SITE OR CLEAVAGE SITE
	Synthetic	:	YES

Molecule 2 - SITE I OF RES DNA
	Chains	:	D, F
	Engineered	:	YES
	Synonym	:	CROSSOVER SITE OR CLEAVAGE SITE
	Synthetic	:	YES

Molecule 3 - SITE I OF RES DNA
	Chains	:	E
	Engineered	:	YES
	Synonym	:	CROSSOVER SITE OR CLEAVAGE SITE
	Synthetic	:	YES

Molecule 4 - PROTEIN (GAMMA DELTA RESOLVASE)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	TNPR
	Expression System Plasmid	:	MGH285
	Expression System Strain	:	AR120
	Expression System Taxid	:	562
	Gene	:	TNPR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	STRAINS THAT CONTAIN F EPISOME
	Synonym	:	GD RESOLVASE

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1GDT)

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

(no "Cis Peptide Bond" information available for 1GDT)

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECOMBINASES_3	PS51736	Resolvase/invertase-type recombinase catalytic domain profile.	TNR1_ECOLI	2-137	2	A:2-137 B:2-137
2	RECOMBINASES_1	PS00397	Site-specific recombinases active site.	TNR1_ECOLI	6-14	2	A:6-14 B:6-14
3	RECOMBINASES_2	PS00398	Site-specific recombinases signature 2.	TNR1_ECOLI	58-70	2	A:58-70 B:58-70

(no "Exon" information available for 1GDT)

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:183
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           TNR1_ECOLI     1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
               SCOP domains d1gdta2 A:1-140 gamma,delta resolvase, catalytic domain                                                                                     d1gdta1 A:141-183                           SCOP domains
               CATH domains 1gdtA01 A:1-98  [code=3.40.50.1390, no name defined]                                              1gdtA02 A:99-140                          1gdtA03 A:141-183 Homeodomain-like          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhh......eeeee........hhhhhhhhh.....eeee..hhh....hhhhhhhhhhhhh...eeeehhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh....hhhhhhhh...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -RECOMBINASES_3  PDB: A:2-137 UniProt: 2-137                                                                                             ---------------------------------------------- PROSITE (1)
                PROSITE (2) -----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gdt A   1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           TNR1_ECOLI     1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
               SCOP domains d1gdtb2 B:1-140 gamma,delta resolvase, catalytic domain                                                                                     d1gdtb1 B:141-183                           SCOP domains
               CATH domains 1gdtB01 B:1-98  [code=3.40.50.1390, no name defined]                                              1gdtB02 B:99-138                        1gdtB03 B:139-183 Homeodomain-like            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhhh.....................hhhhhhhhh.....eeee..hhh....hhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh....hhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -RECOMBINASES_3  PDB: B:2-137 UniProt: 2-137                                                                                             ---------------------------------------------- PROSITE (1)
                PROSITE (2) -----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gdt B   1 MRLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:DNA  Length:22
                                                      
                 1gdt C   1 GCAGTGTCCGATAATTTATAAA  22
                                    10        20

Chain D from PDB  Type:DNA  Length:13
                                             
                 1gdt D  23 TTATCGGACACTG  35
                                    32

Chain E from PDB  Type:DNA  Length:21
                                                     
                 1gdt E   2 CAGTGTCCGATAATTTATAAA  22
                                    11        21

Chain F from PDB  Type:DNA  Length:13
                                             
                 1gdt F  23 TTATCGGACACTG  35
                                    32

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1390, no name defined] (8)

[unclassified] (4)

1a	1gdtA01	A:1-98
1b	1gdtB01	B:1-98

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

[unclassified] (65)

2a	1gdtB03	B:139-183
2b	1gdtA03	A:141-183

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: [code=1.20.5.40, no name defined] (4)

[unclassified] (4)

3a	1gdtB02	B:99-138
3b	1gdtA02	A:99-140

(no "Pfam Domain" information available for 1GDT)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TNR1_ECOLI | P03012)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000150	recombinase activity	Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
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/Biological Unit
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	TNR1_ECOLI \| P03012	:	1gdr 1ght 1hx7 1res 1ret 1zr2 1zr4 2gm4 2gm5 2rsl

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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

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Exons (0, 0)

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