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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THIOREDOXIN FROM THERMUS THERMOPHILUS
 
Authors :  P. H. Rehse, T. H. Tahirov, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  21 Jan 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Oxidoreductase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. H. Rehse, T. H. Tahirov
Crystallographic Analysis Of Thioredoxin From The Thermophilic Bacteria Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:78 , HIS A:79 , GLU A:130 , ASP B:78BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP A:78 , ASP B:78 , HIS B:79 , GLU B:130BINDING SITE FOR RESIDUE MG B 502
3AC3SOFTWAREHIS A:93 , PRO A:94 , GLY A:95 , LEU A:96 , ARG B:66 , HOH B:694BINDING SITE FOR RESIDUE SO4 A 601
4AC4SOFTWAREARG A:66 , HIS B:93 , PRO B:94 , GLY B:95 , LEU B:96 , HOH B:654 , HOH B:665 , HOH B:671 , HOH B:684BINDING SITE FOR RESIDUE SO4 B 602
5AC5SOFTWAREARG A:112 , ARG A:113BINDING SITE FOR RESIDUE SO4 A 603

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:62 -A:65
2B:62 -B:65

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:105 -Pro A:106
2Val B:105 -Pro B:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V98)

(-) Exons   (0, 0)

(no "Exon" information available for 1V98)

(-) Sequences/Alignments

Asymmetric 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:92
 aligned with Q5SI93_THET8 | Q5SI93 from UniProtKB/TrEMBL  Length:140

    Alignment length:92
                                    58        68        78        88        98       108       118       128       138  
         Q5SI93_THET8    49 GAPLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVDEHPGLAARYGVRSVPTLVLFRRGAPVATWVGASPRRVLEERLRPYLEGR 140
               SCOP domains d1v98a_ A: automated matches                                                                 SCOP domains
               CATH domains 1v98A00 A:49-140 Glutaredoxin                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 1v98 A  49 GAPLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVDEHPGLAARYGVRSVPTLVLFRRGAPVATWVGASPRRVLEERLRPYLEGR 140
                                    58        68        78        88        98       108       118       128       138  


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with Q5SI93_THET8 | Q5SI93 from UniProtKB/TrEMBL  Length:140

    Alignment length:89
                                    60        70        80        90       100       110       120       130         
         Q5SI93_THET8    51 PLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVDEHPGLAARYGVRSVPTLVLFRRGAPVATWVGASPRRVLEERLRPYLEG 139
               SCOP domains d1v98b_ B: automated matches                                                              SCOP domains
               CATH domains 1v98B00 B:51-139 Glutaredoxin                                                             CATH domains
           Pfam domains (1) Thioredoxin-1v98B01 B:51-135                                                         ---- Pfam domains (1)
           Pfam domains (2) Thioredoxin-1v98B02 B:51-135                                                         ---- Pfam domains (2)
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 1v98 B  51 PLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVDEHPGLAARYGVRSVPTLVLFRRGAPVATWVGASPRRVLEERLRPYLEG 139
                                    60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SI93_THET8 | Q5SI93)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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  1v98
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