1Z19 | PD0635 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE(75-356) DIMER BOUND TO A COC' CORE SITE

Authors :   T. Biswas, H. Aihara, M. Radman-Livaja, D. Filman, A. Landy, T. Ellenberger

Date :   03 Mar 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

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

Reference :   T. Biswas, H. Aihara, M. Radman-Livaja, D. Filman, A. Landy, T. Ellenberger
A Structural Basis For Allosteric Control Of Dna Recombination By Lambda Integrase.
Nature V. 435 1059 2005
PubMed-ID: 15973401 | Reference-DOI: 10.1038/NATURE03657
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPTPCPGPTPTPCPAPGPCPTPTPTPTPTPT)-3'*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(PTPTPTPAPTPAPCPTPAPAPGPTPTPGPGPCPAPTPT PA)-3'*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - 33-MER
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - INTEGRASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE-BINDING AND CATATLYTIC DOMAINS
	Gene	:	INT
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE LAMBDA
	Organism Taxid	:	10710

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 17)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (2, 34)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

(no "Site" information available for 1Z19)

(no "SS Bond" information available for 1Z19)

(no "Cis Peptide Bond" information available for 1Z19)

(no "SAP(SNP)/Variant" information available for 1Z19)

(no "PROSITE Motif" information available for 1Z19)

(no "Exon" information available for 1Z19)

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:273
 aligned with VINT_LAMBD | P03700 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:283
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   
           VINT_LAMBD    74 VTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356
               SCOP domains d1z19a_ A: Integrase (Int)                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1z19A01 A:75-174  [code=1.10.150.130, no name defined]                                              --1z19A02 A:177-356 Intergrase catalytic core                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.ee..eeeee......eeeee...ee....eehhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......----------........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z19 A  74 mTLHSWLDRYEKILASRGIKQKTLINYmSKIKAIRRGLPDAPLEDITTKEIAAmLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAESSPCWLRLAmELAVVTGQRVGDLCEmKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISmKETLDKCKEILGGETIIASTRREPLSSGTVSRYFmRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTm----------EWDKIEIK 356
                            |       83        93       103       113       123   |   133       143       153       163       173       183       193       203       213     | 223       233       243       253 |     263       273       283      |293       303       313       323       333    |    -     | 353   
                            |                        101-MSE                   127-MSE                                                                     203-MSE         219-MSE                             255-MSE                            290-MSE                                         338-MSE    349       
                           74-MSE

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with VINT_LAMBD | P03700 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:283
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   
           VINT_LAMBD    74 VTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356
               SCOP domains d1z19b_ B: Integrase (Int)                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1z19B01 B:75-174  [code=1.10.150.130, no name defined]                                              --1z19B02 B:177-356 Intergrase catalytic core                                                                                                                                          CATH domains
           Pfam domains (1) -Ph---Phage_integr_N-1z19B03 B:80-158                                                -------------------Phage_integrase-1z19B01 B:178-349                                                                                                                                           ------- Pfam domains (1)
           Pfam domains (2) -Ph---Phage_integr_N-1z19B04 B:80-158                                                -------------------Phage_integrase-1z19B02 B:178-349                                                                                                                                           ------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhh.ee..eeeee......eeeee...ee....eehhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z19 B  74 mTLHSWLDRYEKILASRGIKQKTLINYmSKIKAIRRGLPDAPLEDITTKEIAAmLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAESSPCWLRLAmELAVVTGQRVGDLCEmKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISmKETLDKCKEILGGETIIASTRREPLSSGTVSRYFmRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTmASQyRDDRGREWDKIEIK 356
                            |       83        93       103       113       123   |   133       143       153       163       173       183       193       203       213     | 223       233       243       253 |     263       273       283      |293       303       313       323       333    |  343       353   
                           74-MSE                    101-MSE                   127-MSE                                                                     203-MSE         219-MSE                             255-MSE                            290-MSE                                         338-MSE              
                                                                                                                                                                                                                                                                                                      342-PTR

Chain C from PDB  Type:DNA  Length:13
                                             
                 1z19 C   1 CTCGTTCAGCTTT  13
                                    10

Chain D from PDB  Type:DNA  Length:20
                                                    
                 1z19 D  14 TTTATACTAAGTTGGCATTA  33
                                    23        33

Chain E from PDB  Type:DNA  Length:33
                                                                 
                 1z19 E  34 TAATGCCAACTTAGTATAAAAAAGCTGAACGAG  66
                                    43        53        63

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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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DNA breaking-rejoining enzymes (47)

Superfamily: DNA breaking-rejoining enzymes (47)

Family: Lambda integrase-like, catalytic core (31)

Protein domain: Integrase (Int) (5)

Bacteriophage lambda [TaxId: 10710] (5)

1a	d1z19a_	A:
1b	d1z19b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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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	1z19A01	A:75-174
1b	1z19B01	B:75-174

Topology: hpI Integrase; Chain A (31)

Homologous Superfamily: Intergrase catalytic core (31)

[unclassified] (26)

2a	1z19B02	B:177-356
2b	1z19A02	A:177-356

Asymmetric Unit(hide GO term definitions)

Chain A,B (VINT_LAMBD | P03700)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008907	integrase activity	Catalysis of the integration of one segment of DNA into another.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.

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Biological Unit
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	1z19
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	VINT_LAMBD \| P03700
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	VINT_LAMBD \| P03700	:	1ae9 1kjk 1m97 1p7d 1z1b 1z1g 2oxo 2wcc 5j0n

Description

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Ligands, Modified Residues, Ions (2, 17)

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