3TR7 - JenaLib

Title :   STRUCTURE OF A URACIL-DNA GLYCOSYLASE (UNG) FROM COXIELLA BURNETII

Authors :   J. Cheung, M. C. Franklin, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn

Date :   09 Sep 11 (Deposition) - 21 Sep 11 (Release) - 20 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Metabolism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498 | Reference-DOI: 10.1002/PROT.24841

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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)
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	(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:219
 aligned with UNG_COXBU | Q83CW4 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
            UNG_COXBU     7 TQTWQTVLGEEKQEPYFQEILDFVKKERKAGKIIYPPQKDIFNALKLTPYEAIKVVILGQDPYHGPNQAHGLAFSVRPGVPAPPSLQNIFKELHADLGVSIPSHGFLEKWAKQGVLLLNAALTVEAGKPQSHANIGWHRFTDKVIESLNDHPEGIVFLLWGSYAQKKSQLITNLRHRILKAPHPSPLSAARGFLGCRHFSKANQLLHEMGRGEIDWALD 225
               SCOP domains d3tr7a_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhhh........hhhhhhh..eeee....ee..........hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhh.....eeeee...............hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------U_DNA_GLYC------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tr7 A   7 TQTWQTVLGEEKQEPYFQEILDFVKKERKAGKIIYPPQKDIFNALKLTPYEAIKVVILGQDPYHGPNQAHGLAFSVRPGVPAPPSLQNIFKELHADLGVSIPSHGFLEKWAKQGVLLLNAALTVEAGKPQSHANIGWHRFTDKVIESLNDHPEGIVFLLWGSYAQKKSQLITNLRHRILKAPHPSPLSAARGFLGCRHFSKANQLLHEmGRGEIDWALD 225
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                                                                                                                                                                          215-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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UNG_COXBU | Q83CW4)

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.

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	Sites
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	Cis Peptide Bonds
		Tyr A:41 - Pro A:42	[ RasMol ]

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	3tr7
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