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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF BSUDG-P56 COMPLEX

Authors :   J. I. Banos-Sanz, L. Mojardin, J. Sanz-Aparicio, B. Gonzalez, M. Salas

Date :   22 Feb 13 (Deposition) - 22 May 13 (Release) - 31 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Hydrolase-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Banos-Sanz, L. Mojardin, J. Sanz-Aparicio, J. M. Lazaro, L. Villar, G. Serrano-Heras, B. Gonzalez, M. Salas
Crystal Structure And Functional Insights Into Uracil-Dna Glycosylase Inhibition By Phage Phi29 Dna Mimic Protein P56
Nucleic Acids Res. V. 41 6761 2013
PubMed-ID: 23671337 | Reference-DOI: 10.1093/NAR/GKT395

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Chains	:	A
	EC Number	:	3.2.2.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-4-UDG-WT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PT7-4
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
	Organism Taxid	:	224308
	Synonym	:	UDG

Molecule 2 - P56
	Chains	:	B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-3-P56-F29
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PT7-3
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS PHAGE PHI29
	Organism Taxid	:	10756
	Synonym	:	LEFT END OF BACTERIOPHAGE PHI-29 CODING FOR 15 POTENTIAL PROTEINS AMONG THESE ARE THE TERMINAL PROTEIN AND THE PROTEINS ENCODED BY THE GENES 1,2 (SUS), 3, AND (PROBABLY) 4

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:165 , ARG A:166 , HIS A:167 , CL A:1227 , HOH A:2317 , SER B:34 , GLU B:37 , VAL B:38	BINDING SITE FOR RESIDUE GOL A1226
2	AC2	SOFTWARE	THR A:186 , HIS A:187 , GOL A:1226 , HOH A:2279 , HOH A:2282	BINDING SITE FOR RESIDUE CL A1227

Asymmetric/Biological Unit

No.	Residues
1	A:103	-	A:221

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:39	-	Pro A:40

(no "SAP(SNP)/Variant" information available for 3ZOQ)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	U_DNA_GLYCOSYLASE	PS00130	Uracil-DNA glycosylase signature.	UNG_BACSU	58-67	1	A:58-67

(no "Exon" information available for 3ZOQ)

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:223
 aligned with UNG_BACSU | P39615 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
            UNG_BACSU     3 QLLQDSWWNQLKEEFEKPYYQELREMLKREYAEQTIYPDSRDIFNALHYTSYDDVKVVILGQDPYHGPGQAQGLSFSVKPGVKQPPSLKNIFLELQQDIGCSIPNHGSLVSWAKQGVLLLNTVLTVRRGQANSHKGKGWERLTDRIIDVLSERERPVIFILWGRHAQMKKERIDTSKHFIIESTHPSPFSARNGFFGSRPFSRANAYLEKMGEAPIDWCIKDL 225
               SCOP domains d3zoqa_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhh......eee.........................hhhhhhhhhhhhhhh.........hhhhhhh.ee.......ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhh.....eeeee......hhhhh....hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------U_DNA_GLYC-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zoq A   3 QLLQDSWWNQLKEEFEKPYYQELREMLKREYAEQTIYPDSRDIFNALHYTSYDDVKVVILGQDPYHGPGQAQGLSFSVKPGVKQPPSLKNIFLELQQDIGCSIPNHGSLVSWAKQGVLLLNTVLTVRRGQANSHKGKGWERLTDRIIDVLSERERPVIFILWGRHAQMKKERIDTSKHFIIESTHPSPFSARNGFFGSRPFSRANAYLEKMGEAPIDWCIKDL 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:48
 aligned with P56_BPPH2 | Q38503 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:48
                                    17        27        37        47        
            P56_BPPH2     8 DSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKV  55
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.....eeeeeeeeehhhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 3zoq B   8 DSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKV  55
                                    17        27        37        47

Chain C from PDB  Type:PROTEIN  Length:53
 aligned with P56_BPPH2 | Q38503 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:53
                                    13        23        33        43        53   
            P56_BPPH2     4 NDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL  56
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeeeeehhhhhhhhhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3zoq C   4 NDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL  56
                                    13        23        33        43        53

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: Uracil-DNA glycosylase-like (59)

Superfamily: Uracil-DNA glycosylase-like (59)

Family: automated matches (8)

Protein domain: automated matches (8)

Bacillus subtilis [TaxId: 224308] (2)

d3zoqa_

(no "CATH Domain" information available for 3ZOQ)

(no "Pfam Domain" information available for 3ZOQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UNG_BACSU | P39615)

molecular function
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	Catalysis of the hydrolysis of any N-glycosyl bond.
	GO:0004844	uracil DNA N-glycosylase activity	Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B,C (P56_BPPH2 | Q38503)

biological process
	GO:0051701		interaction with host		An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:39 - Pro A:40	[ RasMol ]

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	UNG_BACSU \| P39615
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	3.2.2.27
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UniProtKB/Swiss-Prot
	P56_BPPH2 \| Q38503	:	2le2
	UNG_BACSU \| P39615	:	3zor

3zor	STRUCTURE OF BSUDG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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