2GM5 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   AN ACTIVATED, TRUNCATED GAMMA-DELTA RESOLVASE TETRAMER

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 :   2.10

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

Keywords :   Gamma Delta Resolvase, Site Specific Recombination, Recombination (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 - TRANSPOSON GAMMA-DELTA RESOLVASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET DERIVED
	Expression System Strain	:	B834DE3
	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
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2GM5)

(no "SS Bond" information available for 2GM5)

(no "Cis Peptide Bond" information available for 2GM5)

(no "SAP(SNP)/Variant" information available for 2GM5)

Asymmetric/Biological Unit (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:3-128 B:3-123 C:3-125 D:3-127
2	RECOMBINASES_1	PS00397	Site-specific recombinases active site.	TNR1_ECOLI	6-14	4	A:6-14 B:6-11 C:6-9 D:6-14
3	RECOMBINASES_2	PS00398	Site-specific recombinases signature 2.	TNR1_ECOLI	58-70	4	A:58-70 B:58-70 C:58-70 D:58-70

(no "Exon" information available for 2GM5)

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:122
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           TNR1_ECOLI     2 RLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTNE 128
               SCOP domains d2gm5a_ A: gamma,delta resolvase, cat     alytic domain                                                                         SCOP domains
               CATH domains 2gm5A00 A:2-128  [code=3.40.50.1390,      no name defined]                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhh..hhh.eeeee.-----.hhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhh..eeee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: A:3-128 UniProt: 2-137                                                                                     PROSITE (1)
                PROSITE (2) ----RECOMBINA-------------------------------------------RECOMBINASES_---------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm5 A   2 ALFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKA-----DRKGLDLLRmKVKEGDVILVKKLDHLGRDTADmIQLIKEFDAQGVSIRFIDDGISTDSYIGKmVVTILSAVAQAERQRILERTNE 128
                                    11        21        31      |  -  |     51 |      61        71    |   81        91       101    |  111       121       
                                                               38    44       53-MSE                 76-MSE                       106-MSE

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:122
                                    11        21        31        41        51        61        71        81        91       101       111       121  
           TNR1_ECOLI     2 RLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRIL 123
               SCOP domains d2gm5b_ B:    gamma,delta resolvase,      catalytic domain                                                                 SCOP domains
               CATH domains 2gm5B00 B:   2-123  [code=3.40.50.139     0, no name defined]                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..---.hhhhhhhhhhh..hhh.eeeee.-----.hhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhh..eeee....ee..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: B:3-123 UniProt: 2-137                                                                                PROSITE (1)
                PROSITE (2) ----RECOMBINA-------------------------------------------RECOMBINASES_----------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm5 B   2 ALFGYARVST---SLDIQVRALKDAGVKANRIFTDKA-----DRKGLDLLRmKVKEGDVILVKKLDHLGRDTADmIQLIKEFDAQGVSIRFIDDGISTDSYIGKmVVTILSAVAQAERQRIL 123
                                    11   |    21        31      |  -  |     51 |      61        71    |   81        91       101    |  111       121  
                                    11  15                     38    44       53-MSE                 76-MSE                       106-MSE

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
           TNR1_ECOLI     2 RLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILER 125
               SCOP domains d2gm5c_      C: gamma,delta resolvase,    catalytic domain                                                                   SCOP domains
               CATH domains 2gm5C00      C:2-125  [code=3.40.50.13   90, no name defined]                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.-----hhhhhhhhhhh...hhh.eeee...---..hhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhhh.eeee....ee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: C:3-125 UniProt: 2-137                                                                                  PROSITE (1)
                PROSITE (2) ----RECOMBINA-------------------------------------------RECOMBINASES_------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm5 C   2 ALFGYARV-----SLDIQVRALKDAGVKANRIFTDKAS---SDRKGLDLLRmKVKEGDVILVKKLDHLGRDTADmIQLIKEFDAQGVSIRFIDDGISTDSYIGKmVVTILSAVAQAERQRILER 125
                                   | -   |    21        31       | - |      51 |      61        71    |   81        91       101    |  111       121    
                                   9    15                      39  43        53-MSE                 76-MSE                       106-MSE

Chain D from PDB  Type:PROTEIN  Length:117
 aligned with TNR1_ECOLI | P03012 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           TNR1_ECOLI     2 RLFGYARVSTSQQSLDIQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMIQLIKEFDAQGVSIRFIDDGISTDGEMGKMVVTILSAVAQAERQRILERTN 127
               SCOP domains d2gm5d_    D: gamma,delta resolvase,       catalytic domain                                                                    SCOP domains
               CATH domains 2gm5D00    D:2-127  [code=3.40.50.13      90, no name defined]                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.---hhhhhhhhhhhhhh..hhh.eeee.------.hhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhh..eeee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) RECOMBINASES_3  PDB: D:3-127 UniProt: 2-137                                                                                    PROSITE (1)
                PROSITE (2) ----RECOMBINA-------------------------------------------RECOMBINASES_--------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gm5 D   2 ALFGYARV---QQSLDIQVRALKDAGVKANRIFTDK------DRKGLDLLRmKVKEGDVILVKKLDHLGRDTADmIQLIKEFDAQGVSIRFIDDGISTDSYIGKmVVTILSAVAQAERQRILERTN 127
                                   | - |      21        31     |   -  |     51 |      61        71    |   81        91       101    |  111       121      
                                   9  13                      37     44       53-MSE                 76-MSE                       106-MSE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Resolvase-like (37)

Superfamily: Resolvase-like (11)

Family: gamma,delta resolvase, catalytic domain (9)

Protein domain: gamma,delta resolvase, catalytic domain (9)

Escherichia coli [TaxId: 562] (9)

1a	d2gm5a_	A:
1b	d2gm5b_	B:
1c	d2gm5c_	C:
1d	d2gm5d_	D:

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)

Escherichia coli. Organism_taxid: 562. (1)

1a	2gm5B00	B:2-123
1b	2gm5C00	C:2-125
1c	2gm5D00	D:2-127
1d	2gm5A00	A:2-128

(no "Pfam Domain" information available for 2GM5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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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(no "Cis Peptide Bonds" information available for 2gm5)

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	2gm5
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UniProtKB/Swiss-Prot
	TNR1_ECOLI \| P03012	:	1gdr 1gdt 1ght 1hx7 1res 1ret 1zr2 1zr4 2gm4 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
2gm4	AN ACTIVATED, TETRAMERIC GAMMA-DELTA RESOLVASE: HIN CHIMAERA BOUND TO CLEAVED DNA
2rsl	REFINEMENT OF GAMMA DELTA RESOLVASE REVEALS A STRIKINGLY FLEXIBLE MOLECULE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 12)

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SS Bonds (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (4, 4)

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