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(-) Description

Title :  CRYSTAL STRUCTURE OF PEROXIREDOXIN AHP1 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH THIOREDOXIN TRX2
 
Authors :  F. M. Lian, J. Yu, X. X. Ma, X. J. Yu, Y. Chen, C. Z. Zhou
Date :  19 Feb 12  (Deposition) - 11 Apr 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Electron Transport, Oxidoreductase, Peroxiredoxin, Thioredoxin-2, Thioredoxin Fold, Thioredoxin-Like Fold, Alkyl Hydroperoxide Reductase, Oxidoreductase-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. M. Lian, J. Yu, X. X. Ma, X. J. Yu, Y. Chen, C. Z. Zhou
Structural Snapshots Of Yeast Alkyl Hydroperoxide Reductase Ahp1 Peroxiredoxin Reveal A Novel Two-Cysteine Mechanism Of Electron Transfer To Eliminate Reactive Oxygen Species.
J. Biol. Chem. V. 287 17077 2012
PubMed-ID: 22474296  |  Reference-DOI: 10.1074/JBC.M112.357368

(-) Compounds

Molecule 1 - PEROXIREDOXIN TYPE-2
    ChainsA
    EC Number1.11.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET29A-DERIVED
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAHP1, L2916, L9354.5, YLR109W
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainS288C
    SynonymAHPC1, CYTOPLASMIC THIOL PEROXIDASE 3, CTPX 3, PEROXIREDOXIN TYPE II, PEROXISOMAL ALKYL HYDROPEROXIDE REDUCTASE, TPX TYPE II, THIOL-SPECIFIC ANTIOXIDANT II, TSA II, THIOREDOXIN PEROXIDASE TYPE II, THIOREDOXIN REDUCTASE TYPE II
 
Molecule 2 - THIOREDOXIN-2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-DERIVED
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneG7746, TRX1, TRX2, YGR209C
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainS288C
    SynonymTHIOREDOXIN II, TR-II, THIOREDOXIN-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4DSS)

(-) Sites  (0, 0)

(no "Site" information available for 4DSS)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:31 -B:31

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met B:73 -Pro B:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DSS)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TRX2_YEAST1-104  1B:1-104
AHP1_YEAST9-176  1A:9-176
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TRX2_YEAST23-41  1B:23-41
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TRX2_YEAST1-104  2B:1-104
AHP1_YEAST9-176  2A:9-176
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TRX2_YEAST23-41  2B:23-41

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR209C1YGR209C.1VII:913232-912918315TRX2_YEAST1-1041041B:1-104104

(-) Sequences/Alignments

Asymmetric 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:174
 aligned with AHP1_YEAST | P38013 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    
           AHP1_YEAST     3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeee................eeeehhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.......eeeee...hhhhhhh..eeeee..eeee..eeeeee..eeeeeee...........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------THIOREDOXIN_2  PDB: A:9-176 UniProt: 9-176                                                                                                                               PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dss A   3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTSTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with TRX2_YEAST | P22803 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
           TRX2_YEAST     1 MVTQLKSASEYDSALASGDKLVVVDFFATWCGPCKMIAPMIEKFAEQYSDAAFYKLDVDEVSDVAQKAEVSSMPTLIFYKGGKEVTRVVGANPAAIKQAIASNV 104
               SCOP domains d4dssb_ B: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: B:1-104 UniProt: 1-104                                                               PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------THIOREDOXIN_1      --------------------------------------------------------------- PROSITE (3)
               Transcript 1 Exon 1.1  PDB: B:1-104 UniProt: 1-104                                                                    Transcript 1
                 4dss B   1 MVTQLKSASEYDSALASGDKLVVVDFFATWCGPSKMIAPMIEKFAEQYSDAAFYKLDVDEVSDVAQKAEVSSMPTLIFYKGGKEVTRVVGANPAAIKQAIASNV 104
                                    10        20        30        40        50        60        70        80        90       100    

   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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DSS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DSS)

(-) Gene Ontology  (31, 35)

Asymmetric Unit(hide GO term definitions)
Chain A   (AHP1_YEAST | P38013)
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:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
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   (TRX2_YEAST | P22803)
molecular function
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    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:0080058    protein deglutathionylation    The protein modification process in which a glutathione molecule is removed from a protein amino acid by breaking a disulfide linkage.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006890    retrograde vesicle-mediated transport, Golgi to ER    The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
    GO:0000011    vacuole inheritance    The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000324    fungal-type vacuole    A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AHP1_YEAST | P380134dsq 4dsr 4h86 4owy
        TRX2_YEAST | P228032fa4 2hsy 3pin

(-) Related Entries Specified in the PDB File

4dsq 4dsr