2NL8 | PD0883 - JenaLib

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Title :   THE ORIGIN BINDING DOMAIN OF THE SV40 LARGE T ANTIGEN BOUND NON SPECIFICALLY TO A 17 BP PALINDROME DNA (SITES 1 AND 3)

Authors :   D. Martynowski, E. Bochkareva, A. Bochkarev

Date :   19 Oct 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,W
Biol. Unit 1: A,W  (2x)

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

Reference :   E. Bochkareva, D. Martynowski, A. Seitova, A. Bochkarev
Structure Of The Origin-Binding Domain Of Simian Virus 40 Large T Antigen Bound To Dna
Embo J. V. 25 5961 2006
PubMed-ID: 17139255 | Reference-DOI: 10.1038/SJ.EMBOJ.7601452
(for further references see the PDB file header)

Molecule 1 - 18-NT PEN ELEMENT OF THE SV40 DNA ORIGIN
	Chains	:	W
	Engineered	:	YES
	Other Details	:	P2 PENTAMER REPLACED WITH ATCAT
	Synthetic	:	YES

Molecule 2 - LARGE T ANTIGEN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ORIGIN BINDING DOMAIN (RESIDUES 131-259)
	Gene	:	LARGE T ANTIGEN
	Mutation	:	YES
	Organism Scientific	:	SIMIAN VIRUS 40
	Organism Taxid	:	10633
	Strain	:	776

		1	2
Asymmetric Unit	:	A	W
Biological Unit 1 (2x)	:	A	W

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NL8)

(no "Site" information available for 2NL8)

(no "SS Bond" information available for 2NL8)

Asymmetric Unit

No.	Residues
1	Asp A:239	-	Pro A:240

(no "SAP(SNP)/Variant" information available for 2NL8)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	T_AG_OBD	PS51287	Large T-antigen (T-ag) origin-binding domain (OBD) profile.	LT_SV40	139-254	1	A:139-249

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	T_AG_OBD	PS51287	Large T-antigen (T-ag) origin-binding domain (OBD) profile.	LT_SV40	139-254	2	A:139-249

(no "Exon" information available for 2NL8)

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:117
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:117
                                   142       152       162       172       182       192       202       212       222       232       242       
              LT_SV40   133 EDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLP 249
               SCOP domains d2nl8a_ A: The origin DNA-binding domain of SV40 T-antigen                                                            SCOP domains
               CATH domains 2nl8A00 A:133-249  [code=3.40.1310.20, no name defined]                                                               CATH domains
               Pfam domains ---T_Ag_DNA_bind-2nl8A01 A:136-229                                                               -------------------- Pfam domains
         Sec.struct. author .......................eeeeeeeehhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeeehhhhhhhhhh.......eeeee..hhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------T_AG_OBD  PDB: A:139-249 UniProt: 139-254                                                                       PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2nl8 A 133 EDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLSTFSFLICKGVNKEYLMYSALTRDPFSVIEESLP 249
                                   142       152       162       172       182       192       202       212       222       232       242

Chain A from PDB  Type:PROTEIN  Length:117
 aligned with Q98ZP7_SV40 | Q98ZP7 from UniProtKB/TrEMBL  Length:537

    Alignment length:117
                                   142       152       162       172       182       192       202       212       222       232       242       
          Q98ZP7_SV40   133 EDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLP 249
               SCOP domains d2nl8a_ A: The origin DNA-binding domain of SV40 T-antigen                                                            SCOP domains
               CATH domains 2nl8A00 A:133-249  [code=3.40.1310.20, no name defined]                                                               CATH domains
               Pfam domains ---T_Ag_DNA_bind-2nl8A01 A:136-229                                                               -------------------- Pfam domains
         Sec.struct. author .......................eeeeeeeehhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeeehhhhhhhhhh.......eeeee..hhhhhhhhhhhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2nl8 A 133 EDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLSTFSFLICKGVNKEYLMYSALTRDPFSVIEESLP 249
                                   142       152       162       172       182       192       202       212       222       232       242

Chain W from PDB  Type:DNA  Length:18
                                                  
                 2nl8 W  10 CGAGGCCATCATGGCCTC  27
                                    19

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Replication Protein E1; Chain: A, (19)

Homologous Superfamily: [code=3.40.1310.20, no name defined] (15)

[unclassified] (4)

2nl8A00

A:133-249

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Rep (10)

Family: T_Ag_DNA_bind (8)

Simian virus 40 (SV40) (7)

T_Ag_DNA_bind-2nl8A01

A:136-229

Asymmetric Unit(hide GO term definitions)

Chain A (Q98ZP7_SV40 | Q98ZP7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Chain A (LT_SV40 | P03070)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006268	DNA unwinding involved in DNA replication	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
	GO:0039686	bidirectional double-stranded viral DNA replication	A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039645	modulation by virus of host G1/S transition checkpoint	Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
	GO:0060153	modulation by virus of host cell cycle	Any viral process that modulates the rate or extent of progression through the cell cycle.
	GO:0039648	modulation by virus of host protein ubiquitination	Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
	GO:0039649	modulation by virus of host ubiquitin-protein ligase activity	The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0039576	suppression by virus of host JAK1 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity. In the host, binding of a ligand to a receptor triggers activation of JAK proteins, which phosphorylate tyrosine residues on the receptor creating sites for STAT proteins to bind, which are in turn phosphorylated and activated by JAK proteins. By blocking JAK1 activity, many viruses block the host signal transduction pathway.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2nl8)

	Sites
(no "Sites" information available for 2nl8)

	Cis Peptide Bonds
		Asp A:239 - Pro A:240	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 1)

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