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(-) Description

Title :  SOLUTION STRUCTURE OF A THIOREDOXIN-LIKE PROTEIN IN THE OXIDIZED FORM
 
Authors :  X. Zhang, B. Xia, C. Jin
Date :  29 Sep 05  (Deposition) - 17 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (11x)
Keywords :  Thioredoxin-Like, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, Y. Hu, X. Guo, E. Lescop, Y. Li, B. Xia, C. Jin
The Bacillus Subtilis Ykuv Is A Thiol-Disulfide Oxidoreductase Revealed By Its Redox Structures And Activity
J. Biol. Chem. V. 281 8296 2006
PubMed-ID: 16418167  |  Reference-DOI: 10.1074/JBC.M512015200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YKUV PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-148
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: TRXY

 Structural Features

(-) Chains, Units

  
NMR Structure (11x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B5Y)

(-) Sites  (0, 0)

(no "Site" information available for 2B5Y)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:41 -A:44

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B5Y)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.YKUV_BACSU1-145  1A:1-145

(-) Exons   (0, 0)

(no "Exon" information available for 2B5Y)

(-) 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:148
 aligned with YKUV_BACSU | O31699 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
           YKUV_BACSU     1 MKLRQPMPELTGEKAWLNGEVTREQLIGEKPTLIHFWSISCHLCKEAMPQVNEFRDKYQDQLNVVAVHMPRSEDDLDPGKIKETAAEHDITQPIFVDSDHALTDAFENEYVPAYYVFDKTGQLRHFQAGGSGMKMLEKRVNRVLAETE 148
               SCOP domains d2b5ya_ A: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee....hhhhhh....eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.....eee...hhhhhhh......eeeee.....eeeeee.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: A:1-145 UniProt: 1-145                                                                                                       --- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b5y A   1 MKLRQPMPELTGEKAWLNGEVTREQLIGEKPTLIHFWSISCHLCKEAMPQVNEFRDKYQDQLNVVAVHMPRSEDDLDPGKIKETAAEHDITQPIFVDSDHALTDAFENEYVPAYYVFDKTGQLRHFQAGGSGMKMLEKRVNRVLAETE 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (0, 0)

(no "CATH Domain" information available for 2B5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B5Y)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (YKUV_BACSU | O31699)
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: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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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: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: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: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.

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 Related Entries

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        YKUV_BACSU | O31699: 2b5x

(-) Related Entries Specified in the PDB File

2b5x STRUCTURE IN THE REDUCED FORM