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(-) Description

Title :  CRYSTAL STRUCTURE OF THIOL PEROXIDASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  B. S. Rho, J. D. Pedelacq, L. W. Hung, J. M. Holton, D. Vigil, S. I. Kim, M. S T. C. Terwilliger, Tb Structural Genomics Consortium (Tbsgc)
Date :  28 Oct 04  (Deposition) - 07 Dec 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Thioredoxin Fold, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. S. Rho, L. W. Hung, J. M. Holton, D. Vigil, S. I. Kim, M. S. Park, T. C. Terwilliger, J. D. Pedelacq
Functional And Structural Characterization Of A Thiol Peroxidase From Mycobacterium Tuberculosis.
J. Mol. Biol. V. 361 850 2006
PubMed-ID: 16884737  |  Reference-DOI: 10.1016/J.JMB.2006.05.076

(-) Compounds

Molecule 1 - THIOL PEROXIDASE
    ChainsA
    EC Number1.11.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28 DERIVATIVE
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTPX
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CSX1Mod. Amino AcidS-OXY CYSTEINE
2NH42Ligand/IonAMMONIUM ION
3YT33Ligand/IonYTTRIUM (III) ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CSX1Mod. Amino AcidS-OXY CYSTEINE
2NH42Ligand/IonAMMONIUM ION
3YT33Ligand/IonYTTRIUM (III) ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CSX2Mod. Amino AcidS-OXY CYSTEINE
2NH44Ligand/IonAMMONIUM ION
3YT36Ligand/IonYTTRIUM (III) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:16 , GLU A:149 , YT3 A:203 , HOH A:470BINDING SITE FOR RESIDUE YT3 A 201
2AC2SOFTWAREASP A:40BINDING SITE FOR RESIDUE YT3 A 202
3AC3SOFTWAREGLU A:16 , GLU A:149 , YT3 A:201 , HOH A:548BINDING SITE FOR RESIDUE YT3 A 203
4AC4SOFTWAREASP A:56 , ALA A:88BINDING SITE FOR RESIDUE NH4 A 301
5AC5SOFTWAREHOH A:509BINDING SITE FOR RESIDUE NH4 A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_MYCTO18-165  1A:18-165
TPX_MYCTU18-165  1A:18-165
2TPXPS01265 Tpx family signature.TPX_MYCTO82-93  1A:82-93
TPX_MYCTU82-93  1A:82-93
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_MYCTO18-165  1A:18-165
TPX_MYCTU18-165  1A:18-165
2TPXPS01265 Tpx family signature.TPX_MYCTO82-93  1A:82-93
TPX_MYCTU82-93  1A:82-93
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_MYCTO18-165  2A:18-165
TPX_MYCTU18-165  2A:18-165
2TPXPS01265 Tpx family signature.TPX_MYCTO82-93  2A:82-93
TPX_MYCTU82-93  2A:82-93

(-) Exons   (0, 0)

(no "Exon" information available for 1XVQ)

(-) 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:160
 aligned with TPX_MYCTO | P9WG34 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:166
                                                                                                                                                                                             165  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |  
            TPX_MYCTO     2 AQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA--   -
               SCOP domains d1xvqa_ A: Thiol peroxidase Tpx                                                                                                                                        SCOP domains
               CATH domains 1xvqA00 A:2-167 Glutaredoxin                                                                                                                                           CATH domains
               Pfam domains -----------------Redoxin-1xvqA01 A:19-160                                                                                                                      ------- Pfam domains
         Sec.struct. author ..........................eee.....eee.hhhh...eeeee.........hhhhhhhhhhhhhh..eeeeee..hhhhhh...------.eeeee....hhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhh. 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
                 1xvq A   2 AQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLcVSKDLPFAQKRFC------NVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGATS 167
                                    11        21        31        41        51        61        71        81        91 |     101       111       121       131       141       151       161      
                                                                                                         80-CSX       93    100                                                                   

Chain A from PDB  Type:PROTEIN  Length:160
 aligned with TPX_MYCTU | P9WG35 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:166
                                                                                                                                                                                             165  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |  
            TPX_MYCTU     2 AQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLCVSKDLPFAQKRFCGAEGTENVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGA--   -
               SCOP domains d1xvqa_ A: Thiol peroxidase Tpx                                                                                                                                        SCOP domains
               CATH domains 1xvqA00 A:2-167 Glutaredoxin                                                                                                                                           CATH domains
               Pfam domains -----------------Redoxin-1xvqA01 A:19-160                                                                                                                      ------- Pfam domains
         Sec.struct. author ..........................eee.....eee.hhhh...eeeee.........hhhhhhhhhhhhhh..eeeeee..hhhhhh...------.eeeee....hhhhhh...............eeeee.....eeeeee........hhhhhhhhhhhh. 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
                 1xvq A   2 AQITLRGNAINTVGELPAVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCATSVRTFDERAAASGATVLcVSKDLPFAQKRFC------NVMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNVAYTELVPEIAQEPNYEAALAALGATS 167
                                    11        21        31        41        51        61        71        81        91 |     101       111       121       131       141       151       161      
                                                                                                         80-CSX       93    100                                                                   

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (19, 27)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain A   (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.

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 Related Entries

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

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        TPX_MYCTO | P9WG341y25
        TPX_MYCTU | P9WG351y25

(-) Related Entries Specified in the PDB File

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