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(-) Description

Title :  1-CYS PEROXIDOXIN FROM PLASMODIUM YOELLI
 
Authors :  M. Vedadi, S. Sharma, S. Houston, J. Lew, G. Wasney, M. Amani, X. Xu, J. Bray, M. Sundstrom, C. Arrowsmith, A. Edwards, R. Hui, A. Bochkarev Structural Genomics Consortium (Sgc)
Date :  01 Sep 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Unknown Function, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vedadi, J. Lew, J. Artz, M. Amani, Y. Zhao, A. Dong, G. A. Wasney, M. Gao, T. Hills, S. Brokx, W. Qiu, S. Sharma, A. Diassiti, Z. Alam, M. Melone, A. Mulichak, A. Wernimont, J. Bray, P. Loppnau, O. Plotnikova, K. Newberry, E. Sundararajan, S. Houston, J. Walker, W. Tempel, A. Bochkarev, I. Kozieradzki, A. Edwards, C. Arrowsmith, D. Roos, K. Kain, R. Hui
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-CYS PEROXIREDOXIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15-TEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PY04285
    Organism Scientific: PLASMODIUM YOELII
    Organism Taxid: 5861
    Other Details: PET15-TEV IS A MODIFICATION OF PET15B (NOVAGEN) WITH THROMBIN SITE REPLACED WITH TEV SITE.

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1XCC)

(-) Sites  (0, 0)

(no "Site" information available for 1XCC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XCC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XCC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XCC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XCC)

(-) Exons   (0, 0)

(no "Exon" information available for 1XCC)

(-) 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:219
 aligned with Q86SB3_9APIC | Q86SB3 from UniProtKB/TrEMBL  Length:220

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
         Q86SB3_9APIC     2 GYHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
               SCOP domains d1xcca_ A: 1-Cys peroxiredoxin                                                                                                                                                                                              SCOP domains
               CATH domains 1xccA01 A:2-152 Glutaredoxin                                                                                                                           1xccA02 A:153-220 Antioxidant, Horf6; Chain A, domain2               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee........eehhhhh...eeeee......hhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhh.......eee...hhhhhhhh.eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee....hhhhhhhhh...eee..........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcc A   2 GYHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q86SB3_9APIC | Q86SB3 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
         Q86SB3_9APIC     3 YHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
               SCOP domains d1xccb_ B: 1-Cys peroxiredoxin                                                                                                                                                                                             SCOP domains
               CATH domains 1xccB01 B:3-152 Glutaredoxin                                                                                                                          1xccB02 B:153-220 Antioxidant, Horf6; Chain A, domain2               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee........eehhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh........eee...hhhhhhhh.eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee....hhhhh.......eee..........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcc B   3 YHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with Q86SB3_9APIC | Q86SB3 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
         Q86SB3_9APIC     3 YHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
               SCOP domains d1xccc_ C: 1-Cys peroxiredoxin                                                                                                                                                                                             SCOP domains
               CATH domains 1xccC01 C:3-152 Glutaredoxin                                                                                                                          1xccC02 C:153-220 Antioxidant, Horf6; Chain A, domain2               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee........eehhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhh.......eee...hhhhhhhh.eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee....hhhhh.......eee..........eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcc C   3 YHLGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with Q86SB3_9APIC | Q86SB3 from UniProtKB/TrEMBL  Length:220

    Alignment length:216
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
         Q86SB3_9APIC     5 LGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
               SCOP domains d1xccd_ D: 1-Cys peroxiredoxin                                                                                                                                                                                           SCOP domains
               CATH domains 1xccD01 D:5-152 Glutaredoxin                                                                                                                        1xccD02 D:153-220 Antioxidant, Horf6; Chain A, domain2               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee........eehhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh........eee...hhhhhhh..eeeeee.....eee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.ee..........eee.......hhhhhh....ee..........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xcc D   5 LGATFPNFTAKASGIDGDFELYKYIENSWAILFSHPNDFTPVCTTELAELGKMHEDFLKLNCKLIGFSCNSKESHDKWIEDIKYYGKLNKWEIPIVCDESRELANKLKIMDEQEKDITGLPLTCRCLFFISPEKKIKATVLYPATTGRNAHEILRVLKSLQLTYTTPVATPVNWNEGDKCCVIPTLQDDEISKHFKNEITKVEMPSKKKYLRFVNL 220
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XCC)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q86SB3_9APIC | Q86SB3)
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:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
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

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        Q86SB3_9APIC | Q86SB3: 3tb2

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