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(-) Description

Title :  STRUCTURE OF MYCOBACTERIAL THIOL PEROXIDASE TPX
 
Authors :  M. Stehr, B. Hoffmann, T. Jger, M. Singh, H. J. Hecht
Date :  20 Nov 04  (Deposition) - 20 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Stehr, H. J. Hecht, T. Jager, L. Flohe, M. Singh
Structure Of The Inactive Variant C60S Of Mycobacterium Tuberculosis Thiol Peroxidase
Acta Crystallogr. , Sect. D V. 62 563 2006
PubMed-ID: 16627951  |  Reference-DOI: 10.1107/S0907444906008249

(-) Compounds

Molecule 1 - PROBABLE THIOL PEROXIDASE
    ChainsA, B
    EC Number1.11.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B(+)
    Expression System StrainTUNER (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRV1932 TPX
    MutationYES
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    SynonymTHIOL PEROXIDASE RV1932 TPX PEROXIREDOXIN

 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
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:57 , PRO A:58 , VAL A:59 , SER A:60 , ARG A:130BINDING SITE FOR RESIDUE ACT A 1200
2AC2SOFTWARETHR B:57 , PRO B:58 , VAL B:59 , SER B:60 , ARG B:130 , HOH B:2298BINDING SITE FOR RESIDUE ACT B 2200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y25)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_MYCTO18-165
 
  2A:18-165
B:18-165
TPX_MYCTU18-165
 
  2A:18-165
B:18-165
2TPXPS01265 Tpx family signature.TPX_MYCTO82-93
 
  2A:82-93
B:82-93
TPX_MYCTU82-93
 
  2A:82-93
B:82-93

(-) Exons   (0, 0)

(no "Exon" information available for 1Y25)

(-) 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:165
 aligned with TPX_MYCTO | P9WG34 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            TPX_MYCTO     1 MAQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
               SCOP domains --d1y25a1 A:3-165 Thiol peroxidase Tpx                                                                                                                                SCOP domains
               CATH domains 1y25A00 A:1-165 Glutaredoxin                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...............eee.....eee.hhhh...eeeee.....hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee....hhhhhh.....hhhhh.....eeeee.....eeeeee........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------THIOREDOXIN_2  PDB: A:18-165 UniProt: 18-165                                                                                                         PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y25 A   1 HSQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVSATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

Chain A from PDB  Type:PROTEIN  Length:165
 aligned with TPX_MYCTU | P9WG35 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            TPX_MYCTU     1 MAQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
               SCOP domains --d1y25a1 A:3-165 Thiol peroxidase Tpx                                                                                                                                SCOP domains
               CATH domains 1y25A00 A:1-165 Glutaredoxin                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...............eee.....eee.hhhh...eeeee.....hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee....hhhhhh.....hhhhh.....eeeee.....eeeeee........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: A:18-165 UniProt: 18-165                                                                                                         PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y25 A   1 HSQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVSATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with TPX_MYCTO | P9WG34 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            TPX_MYCTO     1 MAQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
               SCOP domains d1y25b_ B: Thiol peroxidase Tpx                                                                                                                                       SCOP domains
               CATH domains 1y25B00 B:1-165 Glutaredoxin                                                                                                                                          CATH domains
           Pfam domains (1) ------------------Redoxin-1y25B01 B:19-160                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) ------------------Redoxin-1y25B02 B:19-160                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author ..eeee..eeee...............eee.....eee.hhhh...eeeee.....hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh....eeee....hhhhhh...............eeeee.....eeeeee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------THIOREDOXIN_2  PDB: B:18-165 UniProt: 18-165                                                                                                         PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y25 B   1 HSQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVSATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with TPX_MYCTU | P9WG35 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            TPX_MYCTU     1 MAQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
               SCOP domains d1y25b_ B: Thiol peroxidase Tpx                                                                                                                                       SCOP domains
               CATH domains 1y25B00 B:1-165 Glutaredoxin                                                                                                                                          CATH domains
           Pfam domains (1) ------------------Redoxin-1y25B01 B:19-160                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) ------------------Redoxin-1y25B02 B:19-160                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author ..eeee..eeee...............eee.....eee.hhhh...eeeee.....hhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh....eeee....hhhhhh...............eeeee.....eeeeee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------THIOREDOXIN_2  PDB: B:18-165 UniProt: 18-165                                                                                                         PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------TPX         ------------------------------------------------------------------------ PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y25 B   1 HSQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVSATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

   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  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPX_MYCTO | P9WG34)
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: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: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: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.

Chain A,B   (TPX_MYCTU | P9WG35)
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:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    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:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
    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:0052060    evasion or tolerance by symbiont of host-produced nitric oxide    The process in which an organism avoids the effects of nitric oxide produced as a defense response by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0051409    response to nitrosative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

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        TPX_MYCTO | P9WG341xvq
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(-) Related Entries Specified in the PDB File

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