Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PEROXIREDOXIN AHP1 FROM SACCHAROMYCES CEREVISIAE IN OXIDIZED FORM
 
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 :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxidoreductase, Peroxiredoxin, Peroxidase, Thioredoxin-Like Fold, Alkyl Hydroperoxide Reductase (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
    Chains: A, B, C, D
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-DERIVED
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AHP1, L2916, L9354.5, YLR109W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: AHPC1, 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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4DSQ)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:31 -B:62
2A:62 -B:31
3C:31 -D:62
4C:62 -D:31

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DSQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.AHP1_YEAST9-176
 
 
 		  4A:9-176
B:9-176
C:9-176
D:9-176
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.AHP1_YEAST9-176
 
 
 		  2A:9-176
B:9-176
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.AHP1_YEAST9-176
 
 
 		  2-
-
C:9-176
D:9-176

(-) Exons   (0, 0)

(no "Exon" information available for 4DSQ)

(-) 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.....hhhhh......eeeehhhhhhhh.eeeeee............hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.......eeeee...hhhhhhh..eeeee..eeee..eeeeee..eeeeeee...........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------THIOREDOXIN_2  PDB: A:9-176 UniProt: 9-176                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dsq A   3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 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: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.....hhhhh......eeeehhhhhhhh.eeeeee............hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.......eeeee...hhhhhhh..eeeee..eeee..eeeeee..eeeeeee...........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------THIOREDOXIN_2  PDB: B:9-176 UniProt: 9-176                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dsq B   3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    


Chain C 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.....hhhhh......eeeehhhhhhhh.eeeeee............hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh......eeeee...hhhhhhh..eeeee..eeee..eeeeee..eeeeeee...........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------THIOREDOXIN_2  PDB: C:9-176 UniProt: 9-176                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dsq C   3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    


Chain D 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.....hhhhh......eeeehhhhhhhh.eeeeee............hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.......eeeee...hhhhhhh..eeeee..eeee..eeeeee..eeeeeee...........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------THIOREDOXIN_2  PDB: D:9-176 UniProt: 9-176                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dsq D   3 DLVNKKFPAGDYKFQYIAISQSDADSESCKMPQTVEWSKLISENKKVIITGAPAAFSPTCTVSHIPGYINYLDELVKEKEVDQVIVVTVDNPFANQAWAKSLGVKDTTHIKFASDPGCAFTKSIGFELAVGDGVYWSGRWAMVVENGIVTYAAKETNPGTDVTVSSVESVLAHL 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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  (0, 0)

(no "SCOP Domain" information available for 4DSQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4dsq)
 
  Sites
(no "Sites" information available for 4dsq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dsq)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4dsq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AHP1_YEAST | P38013
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.15
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AHP1_YEAST | P38013
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AHP1_YEAST | P38013: 4dsr 4dss 4h86 4owy

(-) Related Entries Specified in the PDB File

4dsr 4dss