2GM4 | PD0797 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   AN ACTIVATED, TETRAMERIC GAMMA-DELTA RESOLVASE: HIN CHIMAERA BOUND TO CLEAVED DNA

Authors :   S. Kamtekar, R. S. Ho, W. Li, T. A. Steitz

Date :   05 Apr 06 (Deposition) - 27 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

Chains :   Asym. Unit : A,B,I,J,K,X,Y,Z
Biol. Unit 1: A,B,I,J,K,X,Y,Z  (2x)

Keywords :   Gamma Delta Resolvase, Protein Dna Complex, Site Specific Recombination, Recombination, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kamtekar, R. S. Ho, M. J. Cocco, W. Li, S. V. Wenwieser, M. R. Boocock, N. D. Grindley, T. A. Steitz
Implications Of Structures Of Synaptic Tetramers Of Gamma Delta Resolvase For The Mechanism Of Recombination.
Proc. Natl. Acad. Sci. Usa V. 103 10642 2006
PubMed-ID: 16807292 | Reference-DOI: 10.1073/PNAS.0604062103

*Molecule 1 - 5'-D(CPAPGPTPGPTPCPCPGPAPTPAPAPTPTPTPAPTP APAPA)-3'**
	Chains	:	X, Z, J, I
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(TPTPAPTPCPGPGPAPCPAPCPTPG)-3'**
	Chains	:	Y, K
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - TRANSPOSON GAMMA-DELTA RESOLVASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET25B
	Expression System Strain	:	BL21DE3 STAR PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TNPR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRANSPOSON TN1000 RESOLVASE

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	I	J	K	X	Y	Z
Biological Unit 1 (2x)	:	A	B	I	J	K	X	Y	Z

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2GM4)

(no "Site" information available for 2GM4)

(no "SS Bond" information available for 2GM4)

(no "Cis Peptide Bond" information available for 2GM4)

(no "SAP(SNP)/Variant" information available for 2GM4)

Asymmetric 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:3-137 B:3-137
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

Biological Unit 1 (3, 12)

	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	4	A:3-137 B:3-137
2	RECOMBINASES_1	PS00397	Site-specific recombinases active site.	TNR1_ECOLI	6-14	4	A:6-14 B:6-14
3	RECOMBINASES_2	PS00398	Site-specific recombinases signature 2.	TNR1_ECOLI	58-70	4	A:58-70 B:58-70

(no "Exon" information available for 2GM4)

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:179
 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 d2gm4a2 A:1-140 gamma,delta resolvase,     catalytic domain                                                                                 d2gm4a1 A:141-183                           SCOP domains
               CATH domains 2gm4A01 A:1-98  [code=3.40.50.1390, no     name defined]                                          2gm4A02 A:99-137                       2gm4A03 A:138-183 Homeodomain-like             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhh.hhh.eeeee..----.hhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhh.eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -RECOMBINASES_3  PDB: A:3-137 UniProt: 2-137                                                                                             ---------------------------------------------- PROSITE (1)
                PROSITE (2) -----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm4 A   1 MALFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKAS----DRKGLDLLRMKVKEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDSIDTSSAMGRMVVTILSAVAQAERQRILQRTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
                                    10        20        30        |-   |    50        60        70        80        90       100       110       120       130       140       150       160       170       180   
                                                                 39   44

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           TNR1_ECOLI     2 RLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
               SCOP domains d2gm4b2 B:2-140 gamma,delta resolvase,     catalytic domain                                                                                d2gm4b1 B:141-183                           SCOP domains
               CATH domains 2gm4B01 B:2-98  [code=3.40.50.1390, no     name defined]                                         2gm4B02 B:99-137                       2gm4B03 B:138-183 Homeodomain-like             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh...hhh.eeeee..----.hhhhhhhhh......eeee........hhhhhhhhhhhhhhhh.eeee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: B:3-137 UniProt: 2-137                                                                                             ---------------------------------------------- PROSITE (1)
                PROSITE (2) ----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm4 B   2 ALFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKAS----DRKGLDLLRMKVKEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDSIDTSSAMGRMVVTILSAVAQAERQRILQRTNEGRQEAMAKGVVFGRKRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVINESN 183
                                    11        21        31       | -  |     51        61        71        81        91       101       111       121       131       141       151       161       171       181  
                                                                39   44

Chain I from PDB  Type:DNA  Length:3
                                   
                 2gm4 I  20 AAA  22

Chain J from PDB  Type:DNA  Length:17
                                                 
                 2gm4 J   3 AGTGTCCGATAATTTAT  19
                                    12

Chain K from PDB  Type:DNA  Length:12
                                            
                 2gm4 K  23 TTATCGGACACT  34
                                    32

Chain X from PDB  Type:DNA  Length:18
                                                  
                 2gm4 X   2 CAGTGTCCGATAATTTAT  19
                                    11

Chain Y from PDB  Type:DNA  Length:13
                                             
                 2gm4 Y  23 TTATCGGACACTG  35
                                    32

Chain Z from PDB  Type:DNA  Length:3
                                   
                 2gm4 Z  20 AAA  22

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 '\|'

(no "Pfam Domain" information available for 2GM4)

Asymmetric 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 Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2gm4)

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(no "Sites" information available for 2gm4)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gm4)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2gm4
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	TNR1_ECOLI \| P03012
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UniProtKB/Swiss-Prot
	TNR1_ECOLI \| P03012	:	1gdr 1gdt 1ght 1hx7 1res 1ret 1zr2 1zr4 2gm5 2rsl

1gdt	CRYSTAL STRUCTURE OF A SITE-SPECIFIC RECOMBINASE, GAMMA- DELTA RESOLVASE COMPLEXED WITH A 34 BP CLEAVAGE SITE
1zr2	STRUCTURE OF A SYNAPTIC GAMMA-DELTA RESOLVASE TETRAMER COVALENTLY LINKED TO TWO CLEAVED DNAS
1zr4	STRUCTURE OF A SYNAPTIC GAMMA-DELTA RESOLVASE TETRAMER COVALENTLY LINKED TO TWO CLEAVED DNAS
2gm5	AN ACTIVATED, TRUNCATED GAMMA-DELTA RESOLVASE TETRAMER
2rsl	REFINEMENT OF GAMMA DELTA RESOLVASE REVEALS A STRIKINGLY FLEXIBLE MOLECULE

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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PROSITE Motifs (3, 6)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (3, 6)

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Gene Ontology (4, 4)

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