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(-) Description

Title :  ESCHERICHIA COLI THIOL PEROXIDASE (TPX) WILD TYPE DISULFIDE FORM
 
Authors :  A. Hall, P. A. Karplus
Date :  16 Jun 09  (Deposition) - 20 Oct 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Tpx, Peroxiredoxin, Peroxidase, Antioxidant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Hall, B. Sankaran, L. B. Poole, P. A. Karplus
Structural Changes Common To Catalysis In The Tpx Peroxiredoxin Subfamily.
J. Mol. Biol. V. 393 867 2009
PubMed-ID: 19699750  |  Reference-DOI: 10.1016/J.JMB.2009.08.040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOL PEROXIDASE
    ChainsA, B
    EC Number1.11.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROK1
    Expression System StrainXL-1 BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneB1324, JW1317, TPX, YZZJ
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
    StrainK-12 (XL-1 BLUE)
    SynonymSCAVENGASE P20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:62 , SER A:64 , VAL A:65 , ARG A:133 , ILE A:153 , THR A:154 , THR A:155 , GLU A:156 , PRO A:157 , TYR A:159 , HOH A:217 , HOH A:255 , HOH A:281 , HOH A:351 , HOH A:406 , HOH A:590BINDING SITE FOR RESIDUE CIT A 1
2AC2SOFTWARESER B:64 , VAL B:65 , ARG B:133 , ILE B:153 , THR B:154 , THR B:155 , GLU B:156 , PRO B:157 , TYR B:159 , HOH B:253 , HOH B:262 , HOH B:451 , HOH B:497BINDING SITE FOR RESIDUE CIT B 169

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:61 -A:95
2B:61 -B:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HVS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_ECOLI19-168
 
  2A:19-168
B:19-168
2TPXPS01265 Tpx family signature.TPX_ECOLI84-95
 
  2A:84-95
B:84-95

(-) Exons   (0, 0)

(no "Exon" information available for 3HVS)

(-) 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:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvsa_ A: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvsA00 A:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeee.........hhhhhhhhhhhhh...eeeeeee..hhhhhh..........eeeee....hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: A:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvs A   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with TPX_ECOLI | P0A862 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            TPX_ECOLI     2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
               SCOP domains d3hvsb_ B: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvsB00 B:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeee.........hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....eeeee....hhhhhhh...............eeeee.....eeeeee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: B:19-168 UniProt: 19-168                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hvs B   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPX_ECOLI | P0A862)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0032843    hydroperoxide reductase activity    Catalysis of the reaction: 2 RSH + ROOH = RSSR + ROH + H2O. This reaction is the thiol-dependent conversion of an organic hydroperoxide to the corresponding alcohol.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016684    oxidoreductase activity, acting on peroxide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which the peroxide group acts as a hydrogen or electron acceptor.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    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:0008379    thioredoxin peroxidase activity    Catalysis of the reaction: thioredoxin + hydrogen peroxide = thioredoxin disulfide + H2O.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPX_ECOLI | P0A8621qxh 3hvv 3hvx 3i43 4af2

(-) Related Entries Specified in the PDB File

1qxh E. COLI TPX WILD TYPE DISULFIDE FORM AT 2.2 A RESOLUTION
3hvv E. COLI TPX C61S MUTANT AT 1.75 A RESOLUTION
3hvx E. COLI TPX C82S, C95S MUTANT AT 2.21 A RESOLUTION
3i43 E. COLI TPX WILD TYPE DISULFIDE FORM AT 2.8 A RESOLUTION USED TO CONFIRM THE PRESENCE OF AN INTACT DISULFIDE IN 3HVS