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(-) Description

Title :  CRYSTALLOGRAPHIC AND SPECTROSCOPIC CHARACTERIZATION OF SULFOLOBUS SOLFATARICUS TRXA1 PROVIDE INSIGHTS INTO THE DETERMINANTS OF THIOREDOXIN FOLD STABILITY
 
Authors :  L. Esposito, A. Ruggiero, M. Masullo, M. R. Ruocco, A. Lamberti, P. Arca A. Zagari, L. Vitagliano
Date :  09 Aug 11  (Deposition) - 30 Nov 11  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Disulfide Oxidoreductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Esposito, A. Ruggiero, M. Masullo, M. R. Ruocco, A. Lamberti, P. Arcari, A. Zagari, L. Vitagliano
Crystallographic And Spectroscopic Characterizations Of Sulfolobus Solfataricus Trxa1 Provide Insights Into The Determinants Of Thioredoxin Fold Stability.
J. Struct. Biol. V. 177 506 2012
PubMed-ID: 22085748  |  Reference-DOI: 10.1016/J.JSB.2011.10.014

(-) Compounds

Molecule 1 - THIOREDOXIN (TRXA-1)
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TRUNCATED FORM (25-133) OF THIOREDOXIN (TRXA-1)
    Gene: TRXA-1, SSO0368
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:23 , VAL A:29 , VAL C:107 , ASN C:108 , GLN C:110BINDING SITE FOR RESIDUE EDO A 500
2AC2SOFTWAREVAL A:107 , ASN A:108 , GLN A:110 , VAL B:29BINDING SITE FOR RESIDUE EDO A 501
3AC3SOFTWAREHOH A:15 , LYS A:130 , VAL B:32 , THR B:34 , GLU B:36BINDING SITE FOR RESIDUE EDO A 504
4AC4SOFTWAREHOH A:13 , ASP A:28 , THR A:30 , TYR C:131 , HOH C:227BINDING SITE FOR RESIDUE EDO A 506
5AC5SOFTWAREVAL B:107 , ASN B:108 , GLN B:110 , VAL C:29 , HOH C:135BINDING SITE FOR RESIDUE EDO B 502
6AC6SOFTWARETHR A:34 , GLU A:36 , ASN A:37 , HOH C:20 , ASP C:113 , LYS C:130 , HOH C:204BINDING SITE FOR RESIDUE EDO C 503
7AC7SOFTWAREASP B:113 , LYS B:130 , HOH C:6 , GLU C:36 , ASN C:37 , EDO C:507BINDING SITE FOR RESIDUE EDO C 505
8AC8SOFTWARELYS B:130 , HOH C:6 , LEU C:31 , VAL C:32 , EDO C:505BINDING SITE FOR RESIDUE EDO C 507

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:57 -A:60
2B:57 -B:60
3C:57 -C:60

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:100 -Pro A:101
2Ile B:100 -Pro B:101
3Ile C:100 -Pro C:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TCO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TCO)

(-) Exons   (0, 0)

(no "Exon" information available for 3TCO)

(-) 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:106
 aligned with Q980E5_SULSO | Q980E5 from UniProtKB/TrEMBL  Length:133

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
         Q980E5_SULSO    27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
               SCOP domains d3tcoa_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tco A  27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
                                    36        46        56        66        76        86        96       106       116       126      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with Q980E5_SULSO | Q980E5 from UniProtKB/TrEMBL  Length:133

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
         Q980E5_SULSO    27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
               SCOP domains d3tcob_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tco B  27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
                                    36        46        56        66        76        86        96       106       116       126      


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with Q980E5_SULSO | Q980E5 from UniProtKB/TrEMBL  Length:133

    Alignment length:106
                                    36        46        56        66        76        86        96       106       116       126      
         Q980E5_SULSO    27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
               SCOP domains d3tcoc_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tco C  27 EDVTLVLTEENFDEVIRNNKLVLVDCWAEWCAPCHLYEPIYKKVAEKYKGKAVFGRLNVDENQKIADKYSVLNIPTTLIFVNGQLVDSLVGAVDEDTLESTVNKYL 132
                                    36        46        56        66        76        86        96       106       116       126
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TCO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TCO)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q980E5_SULSO | Q980E5)
molecular function
    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: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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