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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SULFIREDOXIN (SRX) IN COMPLEX WITH ATP:MG2+
 
Authors :  T. J Jonsson, M. S. Murray, L. C. Johnson, W. T. Lowther
Date :  25 Apr 08  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cys Sulfinic Acid Reduction, Antioxidant, Atp-Binding, Cytoplasm, Magnesium, Nucleotide-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Jonsson, M. S. Murray, L. C. Johnson, W. T. Lowther
Reduction Of Cysteine Sulfinic Acid In Peroxiredoxin By Sulfiredoxin Proceeds Directly Through A Sulfinic Phosphoryl Ester Intermediate.
J. Biol. Chem. V. 283 23846 2008
PubMed-ID: 18579529  |  Reference-DOI: 10.1074/JBC.M803244200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFIREDOXIN-1
    Chains: A
    EC Number: 1.8.98.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19B
    Expression System Strain: C41(DE3)
    Expression System Vector Type: PLASMID
    Gene: SRXN1, C20ORF139, SRX
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HUMAN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:181 , HOH A:190 , HOH A:191BINDING SITE FOR RESIDUE MG A 2
2AC2SOFTWARELYS A:61 , SER A:64 , LEU A:65 , THR A:68 , SER A:75 , PRO A:77 , GLY A:98 , SER A:99 , HIS A:100 , ARG A:101 , HOH A:172 , HOH A:179 , HOH A:180 , HOH A:190 , HOH A:192BINDING SITE FOR RESIDUE ATP A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CYI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CYI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CYI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CYI)

(-) Exons   (0, 0)

(no "Exon" information available for 3CYI)

(-) 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:107
 aligned with SRXN1_HUMAN | Q9BYN0 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:107
                                    40        50        60        70        80        90       100       110       120       130       
          SRXN1_HUMAN    31 GSIHSGRIAAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGCHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
               SCOP domains d3cyia_ A: Sulfiredoxin                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee...ee.......hhhhhhhhhhhhhhhhhhh..eeeeeee.....eeee...hhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3cyi A  31 MSIHSGRIAAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGSHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
                                    40        50        60        70        80        90       100       110       120       130
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CYI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CYI)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRXN1_HUMAN | Q9BYN0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0016667    oxidoreductase activity, acting on a sulfur group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0032542    sulfiredoxin activity    Catalysis of the reaction: peroxiredoxin-(S-hydroxy-S-oxocysteine) + ATP + 2 R-SH = peroxiredoxin-(S-hydroxycysteine) + ADP + phosphate + R-S-S-R.
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.
    GO:0006979    response to oxidative stress    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 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.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SRXN1_HUMAN | Q9BYN0: 1xw3 1xw4 1yzs 2b6f 2rii 3hy2

(-) Related Entries Specified in the PDB File

1xw3 HUMAN SRX IN COMPLEX WITH PHOSPHATE
1xw4 HUMAN SRX IN COMPLEX WITH ADP
2rii HUMAN PRX I: HUMAN SRX COMPLEX