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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED THIOREDOXIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  A. Ebihara, H. Yanai, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Redox Protein, Electron Transport, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ebihara, H. Yanai, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Oxidized Thioredoxin From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: B834(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-110
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YZU)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:34

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:74 -Pro A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YZU)

(-) Exons   (0, 0)

(no "Exon" information available for 2YZU)

(-) 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:104
 aligned with Q5SHI3_THET8 | Q5SHI3 from UniProtKB/TrEMBL  Length:110

    Alignment length:104
                                    12        22        32        42        52        62        72        82        92       102    
         Q5SHI3_THET8     3 KPIEVTDQNFDETLGQHPLVLVDFWAEWCAPCRMIAPILEEIAKEYEGKLLVAKLDVDENPKTAMRYRVMSIPTVILFKDGQPVEVLVGAQPKRNYQAKIEKHL 106
               SCOP domains d2yzua_ A: automated matches                                                                             SCOP domains
               CATH domains 2yzuA00 A:3-106 Glutaredoxin                                                                             CATH domains
               Pfam domains Thioredoxin-2yzuA01 A:3-105                                                                            - Pfam domains
         Sec.struct. author ..ee....hhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2yzu A   3 KPIEVTDQNFDETLGQHPLVLVDFWAEWCAPCRmIAPILEEIAKEYEGKLLVAKLDVDENPKTAmRYRVmSIPTVILFKDGQPVEVLVGAQPKRNYQAKIEKHL 106
                                    12        22        32   |    42        52        62    |   72        82        92       102    
                                                            36-MSE                         67-MSE|                                  
                                                                                                72-MSE
   Legend:   → Mismatch (orange background)
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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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SHI3_THET8 | Q5SHI3)
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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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  Cis Peptide Bonds
    Ile A:74 - Pro A:75   [ RasMol ]  
 

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