2A4V - JenaLib

Title :   CRYSTAL STRUCTURE OF A TRUNCATED MUTANT OF YEAST NUCLEAR THIOL PEROXIDASE

Authors :   J. Choi, S. Choi, J. -K. Chon, J. Choi, M. -K. Cha, I. -H. Kim, W. Shin

Date :   29 Jun 05 (Deposition) - 14 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Yeast Nuclear Thiol Peroxidase, Atypical 2-Cys Peroxiredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Choi, S. Choi, J. -K. Chon, J. Choi, M. -K. Cha, I. -H. Kim, W. Shin
Crystal Structure Of The C107S/C112S Mutant Of Yeast Nuclear 2-Cys Peroxiredoxin
Proteins V. 61 1146 2005
PubMed-ID: 16245326 | Reference-DOI: 10.1002/PROT.20704
(for further references see the PDB file header)

Compounds

Molecule 1 - PEROXIREDOXIN DOT5
	Chains	:	A
	EC Number	:	1.11.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	DOT5
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	THIOREDOXIN REDUCTASE, NUCLEAR THIOL PEROXIDASE, NTPX, DISRUPTER OF TELOMERE SILENCING PROTEIN 5

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 1)

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:156
 aligned with DOT5_YEAST | P40553 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:156
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208      
           DOT5_YEAST    59 DVNELEIGDPIPDLSLLNEDNDSISLKKITENNRVVVFFVYPRASTPGCTRQACGFRDNYQELKKYAAVFGLSADSVTSQKKFQSKQNLPYHLLSDPKREFIGLLGAKKTPLSGSIRSHFIFVDGKLKFKRVKISPEVSVNDAKKEVLEVAEKFKE 214
               SCOP domains d2a4va1 A:59-214 Peroxiredoxin dot5                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eee.....eeehhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh...eeee...hhhhhhhh...........eeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----THIOREDOXIN_2  PDB: A:63-211 UniProt: 63-211                                                                                                         --- PROSITE
               Transcript 1 Exon 1.1  PDB: A:59-214 UniProt: 1-215 [INCOMPLETE]                                                                                                          Transcript 1
                 2a4v A  59 DVNELEIGDPIPDLSLLNEDNDSISLKKITENNRVVVFFVYPRASTPGSTRQASGFRDNYQELKEYAAVFGLSADSVTSQKKFQSKQNLPYHLLSDPKREFIGLLGAKKTPLSGSIRSHFIFVDGKLKFKRVKISPEVSVNDAKKEVLEVAEKFKE 214
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

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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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DOT5_YEAST | P40553)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
	GO:0051920	peroxiredoxin activity	Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
	GO:0008379	thioredoxin peroxidase activity	Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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