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(-) Description

Title :  ESCHERICHIA COLI THIOL PEROXIDASE (TPX) PEROXIDATIC CYSTEINE TO SERINE MUTANT (C61S)
 
Authors :  A. Hall, B. Sankaran, P. A. Karplus
Date :  16 Jun 09  (Deposition) - 20 Oct 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    Chains: A
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROK1
    Expression System Strain: XL-1 BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B1324, JW1317, TPX, YZZJ
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K-12 (XL-1 BLUE)
    Synonym: SCAVENGASE P20

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HVV)

(-) Sites  (0, 0)

(no "Site" information available for 3HVV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HVV)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HVV)

(-) Sequences/Alignments

Asymmetric Unit
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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 d3hvva_ A: Thiol peroxidase Tpx                                                                                                                                         SCOP domains
               CATH domains 3hvvA00 A:2-168 Glutaredoxin                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee..............eee.....eee.hhhh..eeeeee.......hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh....eeee...hhhhhhhh...............eeeee.....eeeeee........hhhhhhhh... 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
                 3hvv A   2 SQTVHFQGNPVTVANSIPQAGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVSAASVRKFNQLATEIDNTVVLCISADLPFAQSRFCGAEGLNNVITLSTFRNAEFLQAYGVAIADGPLKGLAARAVVVIDENDNVIFSQLVDEITTEPDYEAALAVLKA 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  3hvv
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  TPX_ECOLI | P0A862
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPX_ECOLI | P0A862: 1qxh 3hvs 3hvx 3i43 4af2

(-) Related Entries Specified in the PDB File

1qxh E. COLI TPX WILD TYPE DISULFIDE FORM AT 2.2 A RESOLUTION
3hvs E. COLI TPX WILD TYPE DISULFIDE FORM AT 1.8 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