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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CO-CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS URACIL-DNA GLYCOSYLASE AND THE C-TERMINUS OF THE SINGLE-STRANDED DNA-BINDING PROTEIN

Authors :   N. P. George, J. L. Keck

Date :   01 Nov 11 (Deposition) - 07 Nov 12 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Glycosylase, Ssb C-Terminal, Base Excision Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. P. George, J. L. Keck
Identification Of The Ssb-Interaction Platform Of Deinococcus Radiodurans Uracil-Dna Glycosylase
To Be Published
PubMed: search

Molecule 1 - URACIL-DNA GLYCOSYLASE
	Chains	:	A
	EC Number	:	3.2.2.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B, PNPG078
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DR0689, DR_0689, UNG
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	243230
	Strain	:	R1
	Synonym	:	UDG

Molecule 2 - SINGLE-STRANDED DNA-BINDING PROTEIN
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 290-301
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	1299
	Other Details	:	SYNTHESIZED PEPTIDE
	Synonym	:	SSB, HELIX-DESTABILIZING PROTEIN
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	IOD	2	Ligand/Ion	IODIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:39 , ASN A:225	BINDING SITE FOR RESIDUE IOD A 256
2	AC2	SOFTWARE	SER A:107 , HOH A:297	BINDING SITE FOR RESIDUE IOD A 257

(no "SS Bond" information available for 3UFM)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:57	-	Pro A:58

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

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_DEIRA	76-85	1	A:76-85

(no "Exon" information available for 3UFM)

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:230
 aligned with UNG_DEIRA | Q9RWH9 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:230
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
            UNG_DEIRA    17 PIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATVTE 246
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhh..eeeee....ee..........hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh.....eeeee......hhhhh...hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------U_DNA_GLYC----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ufm A  17 PIIPANLPEDWQEALLPEFSAPYFHELTDFLRQERKEYTIYPPAPDVFNALRYTPLGEVKVLILGQDPYHGPNQAHGLSFSVRPGVRVPPSLRNIYKELTEDIPGFVAPKHGYLRSWAEQGVLLLNAVLTVRAGQANSHQGKGWEHFTDAVIKAVNAKEERVVFILWGSYARKKKKLITGKNHVVIESGHPSPLSEQYFFGTRPFSKTNEALEKAGRGPVEWQLPATVTE 246
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246

Chain B from PDB  Type:PROTEIN  Length:4
 aligned with SSB_DEIRA | Q9RY51 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:4
            SSB_DEIRA   298 DLPF 301
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3ufm B 298 DLPF 301

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 "SCOP Domain" information available for 3UFM)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UNG_DEIRA | Q9RWH9)

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 (SSB_DEIRA | Q9RY51)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	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: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: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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Tyr A:57 - Pro A:58	[ RasMol ]

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	3ufm
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	3.2.2.27
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UniProtKB/Swiss-Prot
	SSB_DEIRA \| Q9RY51	:	1se8 3udg
	UNG_DEIRA \| Q9RWH9	:	2boo 4uqm

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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