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(-) Description

Title :  DOMAIN SWAPPING OF STAPHYLOCOCCUS AUREUS THIOREDOXIN W28A MUTANT
 
Authors :  S. Martinez-Rodriguez, R. Loris, J. Messens
Date :  20 Jun 08  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transport, Swap Domain, Redox Enzymology, Oxidoreductase, Redox-Active Center, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, S. Martinez-Rodriguez, K. Wahni, L. Wyns, R. Loris, J. Messens
Coupling Of Domain Swapping To Kinetic Stability In A Thioredoxin Mutant
J. Mol. Biol. V. 385 1590 2009
PubMed-ID: 19071139  |  Reference-DOI: 10.1016/J.JMB.2008.11.040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21 (AI)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRXA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: TRX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION
2FE2Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:40 , ASP B:80 , HOH B:154 , HOH B:164BINDING SITE FOR RESIDUE CD A 105
2AC2SOFTWAREASP A:80 , HOH A:109 , HOH A:191 , GLU B:40BINDING SITE FOR RESIDUE CD A 106
3AC3SOFTWAREALA A:9 , ASP A:12 , LEU A:104 , HOH A:187 , HOH A:188BINDING SITE FOR RESIDUE CD A 107
4AC4SOFTWAREHIS A:0 , HOH A:162 , HOH A:176 , HOH A:189 , GLU B:41 , HOH B:149BINDING SITE FOR RESIDUE FE A 108
5AC5SOFTWAREGLU B:47 , HOH B:198BINDING SITE FOR RESIDUE CD B 105
6AC6SOFTWAREGLU A:16 , GLU B:41 , HOH B:149 , HOH B:201 , HOH B:202 , HOH B:203BINDING SITE FOR RESIDUE FE B 106

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:29 -A:32
2B:29 -B:32

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:72 -Pro A:73
2Ile B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.THIO_STAAU1-104
 		  2A:1-104
B:1-104
2THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_STAAU21-39
 		  2A:21-39
B:21-39

(-) Exons   (0, 0)

(no "Exon" information available for 3DIE)

(-) 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:106
 aligned with THIO_STAAU | P0A0K6 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:106
                              1                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98      
           THIO_STAAU     - --MAIVKVTDADFDSKVESGVQLVDFWATWCGPCKMIAPVLEELAADYEGKADILKLDVDENPSTAAKYEVMSIPTLIVFKDGQPVDKVVGFQPKENLAEVLDKHL 104
               SCOP domains d3diea_ A: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------3dieA01 A:29-104 Glutaredoxin                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --THIOREDOXIN_2  PDB: A:1-104 UniProt: 1-104                                                               PROSITE (1)
                PROSITE (2) ----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3die A  -1 SHMAIVKVTDADFDSKVESGVQLVDFWATACGPCKMIAPVLEELAADYEGKADILKLDVDENPSTAAKYEVMSIPTLIVFKDGQPVDKVVGFQPKENLAEVLDKHL 104
                                     8        18        28        38        48        58        68        78        88        98      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with THIO_STAAU | P0A0K6 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:106
                              1                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98      
           THIO_STAAU     - --MAIVKVTDADFDSKVESGVQLVDFWATWCGPCKMIAPVLEELAADYEGKADILKLDVDENPSTAAKYEVMSIPTLIVFKDGQPVDKVVGFQPKENLAEVLDKHL 104
               SCOP domains d3dieb_ B: Thioredoxin                                                                                     SCOP domains
               CATH domains ------------------------------3dieB01 B:29-104 Glutaredoxin                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --THIOREDOXIN_2  PDB: B:1-104 UniProt: 1-104                                                               PROSITE (1)
                PROSITE (2) ----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3die B  -1 SHMAIVKVTDADFDSKVESGVQLVDFWATACGPCKMIAPVLEELAADYEGKADILKLDVDENPSTAAKYEVMSIPTLIVFKDGQPVDKVVGFQPKENLAEVLDKHL 104
                                     8        18        28        38        48        58        68        78        88        98
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIO_STAAU | P0A0K6)
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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  3die
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  THIO_STAAU | P0A0K6
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 Related Entries

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

UniProtKB/Swiss-Prot
        THIO_STAAU | P0A0K6: 2o7k 2o85 2o87 2o89

(-) Related Entries Specified in the PDB File

2o7k NON MUTATED PROTEIN
2o85 THE SAME PROTEIN, P31T MUTANT
2o87 THE SAME PROTEIN, P31S MUTANT
2o89 THE SAME PROTEIN, P31T/C32S MUTANT