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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PEROXIREDOXIN I IN COMPLEX WITH SULFIREDOXIN
 
Authors :  T. J. Jonsson, L. C. Johnson, W. T. Lowther
Date :  11 Oct 07  (Deposition) - 08 Jan 08  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,X,Y
Keywords :  Protein-Protein Complex, Engineered Disulfide Bond, Sulfinic Acid Reductase, Antioxidant, Oxidoreductase, Peroxidase, Phosphorylation, Redox-Active Center, Atp-Binding, Magnesium, Nucleotide-Binding, --- -, Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Jonsson, L. C. Johnson, W. T. Lowther
Structure Of The Sulphiredoxin-Peroxiredoxin Complex Reveal An Essential Repair Embrace.
Nature V. 451 98 2008
PubMed-ID: 18172504  |  Reference-DOI: 10.1038/NATURE06415

(-) Compounds

Molecule 1 - PEROXIREDOXIN-1
    ChainsA, B
    EC Number1.11.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17
    Expression System StrainC41(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePRDX1, PAGA, PAGB, TDPX2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTHIOREDOXIN PEROXIDASE 2, THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE 2, PROLIFERATION-ASSOCIATED GENE PROTEIN, PAG, NATURAL KILLER CELL-ENHANCING FACTOR A, NKEF-A
 
Molecule 2 - SULFIREDOXIN-1
    ChainsX, Y
    EC Number1.8.98.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19
    Expression System StrainC41(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSRXN1, C20ORF139, SRX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY X:98 , CYS X:99 , HIS X:100 , ARG X:101BINDING SITE FOR RESIDUE PO4 X 1
2AC2SOFTWAREGLY Y:98 , CYS Y:99 , HIS Y:100 , ARG Y:101BINDING SITE FOR RESIDUE PO4 Y 2

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:52 -X:99
2B:52 -Y:99

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:179 -Gly A:180
2Gly A:180 -Ser A:181
3Ser A:181 -Asp A:182
4Arg X:37 -Ile X:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025050R62GPRDX1_HUMANPolymorphism34034070A/BR62G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX1_HUMAN6-165
 
  2A:6-165
B:6-165

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003192482aENSE00001456866chr1:45987628-45987501128PRDX1_HUMAN-00--
1.3bENST000003192483bENSE00002170473chr1:45984726-45984610117PRDX1_HUMAN1-36362A:3-36
B:3-36
34
34
1.4ENST000003192484ENSE00000771100chr1:45981479-45981326154PRDX1_HUMAN36-87522A:36-87
B:36-87
52
52
1.5aENST000003192485aENSE00000771101chr1:45980667-45980545123PRDX1_HUMAN87-128422A:87-128
B:87-128
42
42
1.6ENST000003192486ENSE00002185232chr1:45980309-45980179131PRDX1_HUMAN128-172452A:128-172
B:128-172
45
45
1.7bENST000003192487bENSE00001845867chr1:45977086-45976719368PRDX1_HUMAN172-199282A:172-186
B:172-187
15
16

(-) 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:184
 aligned with PRDX1_HUMAN | Q06830 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
          PRDX1_HUMAN     3 SGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKP 186
               SCOP domains d2riia_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains 2riiA00 A:3-186 Glutaredoxin                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: A:6-165 UniProt: 6-165                                                                                                                      --------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:3-36            --------------------------------------------------Exon 1.5a  PDB: A:87-128 UniProt: 87-128  -------------------------------------------Exon 1.7b       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: A:36-87 UniProt: 36-87               ----------------------------------------Exon 1.6  PDB: A:128-172 UniProt: 128-172    -------------- Transcript 1 (2)
                 2rii A   3 SGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNSQVIGASVDSHFEHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVSPAGWKPGSDTIKP 186
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with PRDX1_HUMAN | Q06830 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     
          PRDX1_HUMAN     3 SGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKPGSDTIKPD 187
               SCOP domains d2riib_ B: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2riiB00 B:3-187 Glutaredoxin                                                                                                                                                              CATH domains
           Pfam domains (1) -----AhpC-TSA-2riiB01 B:8-142                                                                                                               -------------------1-cysPrx_C-2riiB03         Pfam domains (1)
           Pfam domains (2) -----AhpC-TSA-2riiB02 B:8-142                                                                                                               -------------------1-cysPrx_C-2riiB04         Pfam domains (2)
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh.............eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh..........hhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------G----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: B:6-165 UniProt: 6-165                                                                                                                      ---------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:3-36            --------------------------------------------------Exon 1.5a  PDB: B:87-128 UniProt: 87-128  -------------------------------------------Exon 1.7b        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.4  PDB: B:36-87 UniProt: 36-87               ----------------------------------------Exon 1.6  PDB: B:128-172 UniProt: 128-172    --------------- Transcript 1 (2)
                 2rii B   3 SGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNSQVIGASVDSHFEHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVSPAGWKPGSDTIKPD 187
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     

Chain X from PDB  Type:PROTEIN  Length:106
 aligned with SRXN1_HUMAN | Q9BYN0 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:106
                                    41        51        61        71        81        91       101       111       121       131      
          SRXN1_HUMAN    32 SIHSGRIAAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGCHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
               SCOP domains d2riix_ X: Sulfiredoxin                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee...ee.......hhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2rii X  32 SIHSGRIAAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGCHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
                                    41        51        61        71        81        91       101       111       121       131      

Chain Y from PDB  Type:PROTEIN  Length:99
 aligned with SRXN1_HUMAN | Q9BYN0 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:99
                                    48        58        68        78        88        98       108       118       128         
          SRXN1_HUMAN    39 AAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGCHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
               SCOP domains d2riiy_ Y: Sulfiredoxin                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---ParBc-2riiY01 Y:42-133                                                                      ---- Pfam domains (1)
           Pfam domains (2) ---ParBc-2riiY02 Y:42-133                                                                      ---- Pfam domains (2)
         Sec.struct. author ..eeeee...ee.......hhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2rii Y  39 AAVHNVPLSVLIRPLPSVLDPAKVQSLVDTIREDPDSVPPIDVLWIKGAQGGDYFYSFGGCHRYAAYQQLQRETIPAKLVQSTLSDLRVYLGASTPDLQ 137
                                    48        58        68        78        88        98       108       118       128         

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: ParBc (6)

(-) Gene Ontology  (32, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRDX1_HUMAN | Q06830)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008379    thioredoxin peroxidase activity    Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0034101    erythrocyte homeostasis    Any process of regulating the production and elimination of erythrocytes within an organism.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    GO:0042267    natural killer cell mediated cytotoxicity    The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    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:0042345    regulation of NF-kappaB import into nucleus    Any process that modulates the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0032872    regulation of stress-activated MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    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.
    GO:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
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.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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.

Chain X,Y   (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
        PRDX1_HUMAN | Q068303hy2 4xcs
        SRXN1_HUMAN | Q9BYN01xw3 1xw4 1yzs 2b6f 3cyi 3hy2

(-) Related Entries Specified in the PDB File

1xw3 HUMAN SULFIREDOXIN CRYSTAL STRUCTURE
1xw4 HUMAN SULFIREDOXIN IN COMPLEX WITH ADP