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(-) Description

Title :  CRYSTAL STRUCTURE OF A BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN FROM THE AEROPYRUM PERNIX K1 (FORM-1 CRYSTAL)
 
Authors :  E. Mizohata, K. Murayama, M. Idaka, A. Tatsuguchi, T. Terada, M. Shirou S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  27 Jun 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Antioxidant Enzyme, Reactive Oxygen Species, Thioredoxin Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mizohata, K. Murayama, M. Idaka, A. Tatsuguchi, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Bacterioferritin Comigratory Protein Peroxiredoxin From The Aeropyrum Pernix K1 (Form-1 Crystal)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BACTERIOFERRITIN COMIGRATORY PROTEIN
    Chains: A, B, C, D
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE2125
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1
    Synonym: BACTERIOFERRITIN COMIGRATORY PROTEIN PEROXIREDOXIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2CX3)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:49 -A:54
2B:49 -B:54
3C:49 -C:54
4D:49 -D:54

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CX3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CX3)

(-) Exons   (0, 0)

(no "Exon" information available for 2CX3)

(-) 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)
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:160
 aligned with Q9YA14_AERPE | Q9YA14 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q9YA14_AERPE     1 MVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 160
               SCOP domains d2cx3a1 A:4-163 Bacterioferritin comigratory protein                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.....eeehhhhhh....eeeee.......ee....ee..hhhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx3 A   4 LVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    13        23        33        43        53      | 63        73        83        93       103       113    |  123       133       143       153       163
                                                                                   60-MSE                                                   118-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q9YA14_AERPE | Q9YA14 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         Q9YA14_AERPE     - -MVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 160
               SCOP domains d2cx3b_ B: Bacterioferritin comigratory protein                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eeehhhhhh....eeeee.......ee....ee..hhhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx3 B   3 GLVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    12        22        32        42        52       |62        72        82        92       102       112     | 122       132       142       152       162 
                                                                                    60-MSE                                                   118-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:160
 aligned with Q9YA14_AERPE | Q9YA14 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q9YA14_AERPE     1 MVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 160
               SCOP domains d2cx3c_ C: Bacterioferritin comigratory protein                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.....eeehhhhhh....eeeee.......ee....ee..hhhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee.eeeeee.....eeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx3 C   4 LVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    13        23        33        43        53      | 63        73        83        93       103       113    |  123       133       143       153       163
                                                                                   60-MSE                                                   118-MSE                                         


Chain D from PDB  Type:PROTEIN  Length:160
 aligned with Q9YA14_AERPE | Q9YA14 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q9YA14_AERPE     1 MVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 160
               SCOP domains d2cx3d_ D: Bacterioferritin comigratory protein                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.....eeehhhhhh....eeeee.......ee....ee..hhhhhhhhh..eeeeee..hhhhhhhhhhhh....eeee...hhhhhhh..eeeee..eeeee..eeeee.....eeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cx3 D   4 LVELGEKAPDFTLPNQDFEPVNLYEVLKRGRPAVLIFFPAAFSPVCTKELCTFRDKmAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLNEPDYDEVVREANKIAGELV 163
                                    13        23        33        43        53      | 63        73        83        93       103       113    |  123       133       143       153       163
                                                                                   60-MSE                                                   118-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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CX3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9YA14_AERPE | Q9YA14)
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.
biological process
    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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9YA14_AERPE | Q9YA14: 2cx4 4gqc 4gqf

(-) Related Entries Specified in the PDB File

2cx4 THE SAME PROTEIN OF DIFFERENT SPACE GROUP RELATED ID: APE001002125.1 RELATED DB: TARGETDB