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(-) Description

Title :  CRYSTAL STRUCTURE OF THIOREDOXIN MUTANT D47E IN HEXAGONAL (P61) SPACE GROUP
 
Authors :  J. A. Gavira, R. Godoy-Ruiz, B. Ibarra-Molero, J. M. Sanchez-Ruiz
Date :  01 Jun 06  (Deposition) - 15 May 07  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha Beta, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Godoy-Ruiz, J. A. Gavira, B. Ibarra-Molero, J. M. Sanchez-Ruiz
Crystal Structure Of Thioredoxin Mutant D47E In Hexagonal (P61) Space Group
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTK100
    Expression System StrainJF521
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTRXA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:60BINDING SITE FOR RESIDUE MPD A 501
2AC2SOFTWAREALA A:22 , GLY A:51 , LEU A:53 , THR A:54BINDING SITE FOR RESIDUE MPD A 502

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:32 -A:35
2B:32 -B:35

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:75 -Pro A:76
2Ile B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H71)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_ECOLI25-43
 
  2A:24-42
B:24-42
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_ECOLI25-43
 
  1A:24-42
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_ECOLI25-43
 
  1-
B:24-42

(-) Exons   (0, 0)

(no "Exon" information available for 2H71)

(-) 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:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    12        22        32        42        52        62        72        82        92       102       
           THIO_ECOLI     3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 109
               SCOP domains d2h71a_ A: Thioredoxin                                                                                      SCOP domains
               CATH domains 2h71A00 A:2-108 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2h71 A   2 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIAEEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 108
                                    11        21        31        41        51        61        71        81        91       101       

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    12        22        32        42        52        62        72        82        92       102       
           THIO_ECOLI     3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 109
               SCOP domains d2h71b_ B: Thioredoxin                                                                                      SCOP domains
               CATH domains 2h71B00 B:2-108 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhh......eeeeee..ee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2h71 B   2 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIAEEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 108
                                    11        21        31        41        51        61        71        81        91       101       

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H71)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THIO_ECOLI | P0AA25)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THIO_ECOLI | P0AA251f6m 1keb 1m7t 1oaz 1skr 1sks 1skw 1sl0 1sl1 1sl2 1srx 1t7p 1t8e 1tho 1tk0 1tk5 1tk8 1tkd 1txx 1x9m 1x9s 1x9w 1xoa 1xob 1zcp 1zyq 1zzy 2ajq 2bto 2eio 2eiq 2eir 2fch 2fd3 2h6x 2h6y 2h6z 2h70 2h72 2h73 2h74 2h75 2h76 2o8v 2tir 2trx 3dyr 4hu7 4hu9 4hua 4x43 5hr0 5hr1 5hr2 5hr3

(-) Related Entries Specified in the PDB File

1zzy 2fch 2fd3 2h6x 2h6y 2h70 2h72 2h73 2h74 2h75 2h76 2h7z 2trx