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(-) Description

Title :  SOLUTION STRUCTURE OF THIOREDOXIN TYPE H FROM ORYZA SATIVA
 
Authors :  H. Kumeta, H. Ogura, K. Akagi, E. Katoh, F. Inagaki
Date :  09 Jul 04  (Deposition) - 25 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Structural Genomics, Program For Rice Genome Research, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kumeta, H. Ogura, K. Akagi, E. Katoh, F. Inagaki
Solution Structure Of Thioredoxin Type H From Oryza Sativa
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN H-TYPE
    Chains: A
    EC Number: 1.8.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530
    Synonym: TRX-H, PHLOEM SAP 13 KDA PROTEIN-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WMJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TRXH1_ORYSJ1-118  1A:1-118
TRXH_ORYSI1-118  1A:1-118
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TRXH1_ORYSJ32-50  1A:32-50
TRXH_ORYSI32-50  1A:32-50

(-) Exons   (0, 0)

(no "Exon" information available for 1WMJ)

(-) Sequences/Alignments

NMR Structure
   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:122
 aligned with TRXH1_ORYSJ | Q0D840 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
          TRXH1_ORYSJ     1 MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVEAMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA 122
               SCOP domains d1wmja_ A: automated matches                                                                                               SCOP domains
               CATH domains -------1wmjA01 A:8-115 Glutaredoxin                                                                                ------- CATH domains
               Pfam domains -------Thioredoxin-1wmjA01 A:8-112                                                                              ---------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhh......ee...........hhhhhhhhhhhh.....ee.....hhhhhhhhh.........................hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: A:1-118 UniProt: 1-118                                                                            ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------THIOREDOXIN_1      ------------------------------------------------------------------------ PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmj A   1 MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVEAMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain A from PDB  Type:PROTEIN  Length:122
 aligned with TRXH_ORYSI | A2YIW7 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           TRXH_ORYSI     1 MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVEAMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA 122
               SCOP domains d1wmja_ A: automated matches                                                                                               SCOP domains
               CATH domains -------1wmjA01 A:8-115 Glutaredoxin                                                                                ------- CATH domains
               Pfam domains -------Thioredoxin-1wmjA01 A:8-112                                                                              ---------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhh......ee...........hhhhhhhhhhhh.....ee.....hhhhhhhhh.........................hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) THIOREDOXIN_2  PDB: A:1-118 UniProt: 1-118                                                                            ---- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------THIOREDOXIN_1      ------------------------------------------------------------------------ PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmj A   1 MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVEAMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (16, 21)

NMR Structure(hide GO term definitions)
Chain A   (TRXH1_ORYSJ | Q0D840)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    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:0010497    plasmodesmata-mediated intercellular transport    The movement of substances between cells via plasmodesmata. Plasmodesmata is a fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one cell to that of an adjacent cell.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0009409    response to cold    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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    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:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (TRXH_ORYSI | A2YIW7)
molecular function
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ep7 A SAME PROTEIN FROM CHLAMYDOMONAS REINHARDTII
1ert A SAME PROTEIN FROM HUMAN (REDUCED FORM)
1eru A SAME PROTEIN FROM HUMAN (OXIDIZED FORM)
1srx A SAME PROTEIN FROM E. COLI