2JHQ - JenaLib

Title :   CRYSTAL STRUCTURE OF URACIL DNA-GLYCOSYLASE FROM VIBRIO CHOLERAE

Authors :   I. L. U. Raeder, E. Moe, N. P. Willassen, A. O. Smalas, I. Leiros

Date :   23 Feb 07 (Deposition) - 03 Jun 08 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Mutational Analysis, Psychrophilic Enzymes, Ung, Hydrolase, Uracil-Dna N-Glycosylase, Cold Adaptation, Vibrio Salmonicida, Dna Damage, Dna Repair, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. L. U. Raeder, E. Moe, N. P. Willassen, A. O. Smalas, I. Leiros
Structure Of Uracil-Dna N-Glycosylase (Ung) From Vibrio Cholerae. Mapping Temperature Adaptation Through Structural And Mutational Analysis.
Acta Crystallogr. , Sect. F V. 66 130 2010
PubMed-ID: 20124707 | Reference-DOI: 10.1107/S1744309109052063

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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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Chain A from PDB  Type:PROTEIN  Length:223
 aligned with UNG_VIBCH | Q9KPK8 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:223
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
            UNG_VIBCH     4 SLTWHDVIGNEKQQAYFQQTLQFVESQRQAGKVIYPPAKDVFNAFRFTEFGDVKVVILGQDPYHGPNQAHGLCFSVLPGVKTPPSLVNIYKELAQDIPGFQIPPHGYLQSWAQQGVLLLNTVLTVEQGMAHSHANTGWETFTDRVIDALNQHRNGLIFLLWGSHAQKKGQMIDRQRHHVLMAPHPSPLSAHRGFLGCRHFSKTNQLLQAQGIAPINWQPELES 226
               SCOP domains d2jhqa_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2jhqA00 A:4-226 Uracil-DNA Glycosylase, subunit E                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------UDG-2jhqA01 A:50-211                                                                                                                                              --------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh.eeeee.......................hhhhhhhhhhhhhhh..........hhhhhhh.eeeee....ee..........hhhhhhhhhhhhhhhhh...eeeeehhhhhhhh........eeeee......hhhhhhh..hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------U_DNA_GLYC---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jhq A   4 SLTWHDVIGNEKQQAYFQQTLQFVESQRQAGKVIYPPAKDVFNAFRFTEFGDVKVVILGQDPYHGPNQAHGLCFSVLPGVKTPPSLVNIYKELAQDIPGFQIPPHGYLQSWAQQGVLLLNTVLTVEQGMAHSHANTGWETFTDRVIDALNQHRNGLIFLLWGSHAQKKGQMIDRQRHHVLMAPHPSPLSAHRGFLGCRHFSKTNQLLQAQGIAPINWQPELES 226
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UNG_VIBCH | Q9KPK8)

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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