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(-) Description

Title :  STRUCTURE OF A PROBABLE THIOL PEROXIDASE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima, S. K. Burley, New Research Center For Structural Genomics (Nysgxrc)
Date :  21 Jun 03  (Deposition) - 08 Jul 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Thiol, Peroxidase, Nysgxrc, T817, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima
Structure Of A Probable Thiol Peroxidase From Streptococcus Pneumoniae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THIOL PEROXIDASE
    ChainsA, B
    EC Number1.11.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET T7
    Expression System StrainB834 DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTPX
    Organism ScientificSTREPTOCOCCUS PNEUMONIAE
    Organism Taxid1313

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1PSQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TPX_STRP216-162
 
  2A:16-162
B:16-162
TPX_STRPN16-162
 
  2A:16-162
B:16-162
2TPXPS01265 Tpx family signature.TPX_STRP281-92
 
  2A:81-92
B:81-92
TPX_STRPN81-92
 
  2A:81-92
B:81-92

(-) Exons   (0, 0)

(no "Exon" information available for 1PSQ)

(-) 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:163
 aligned with TPX_STRP2 | Q04JB8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRP2     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqa_ A: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqA00 A:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eee.....eee.hhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------THIOREDOXIN_2  PDB: A:16-162 UniProt: 16-162                                                                                                       - PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq A   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            |                                                                               82-MSE             102-MSE                                                         
                            1-MSE                                                                                                                                                              

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRPN | P0C2J8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRPN     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqa_ A: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqA00 A:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................eee.....eee.hhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: A:16-162 UniProt: 16-162                                                                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq A   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE                                                         

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRP2 | Q04JB8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRP2     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqb_ B: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqB00 B:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.................eee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------THIOREDOXIN_2  PDB: B:16-162 UniProt: 16-162                                                                                                       - PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq B   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE                                                         

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with TPX_STRPN | P0C2J8 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   
            TPX_STRPN     1 MVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSMDLPFAQKRWCGAEGLDNAIMLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
               SCOP domains d1psqb_ B: Probable thiol peroxidase PsaD                                                                                                                           SCOP domains
               CATH domains -1psqB00 B:2-163 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.................eee....eehhhhhh..eeeeee.....hhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeee....hhhhhhh............eeeee.....eeeeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: B:16-162 UniProt: 16-162                                                                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------TPX         ----------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1psq B   1 mVTFLGNPVSFTGKQLQVGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSIDTGICSTQTRRFNEELAGLDNTVVLTVSmDLPFAQKRWCGAEGLDNAImLSDYFDHSFGRDYALLINEWHLLARAVFVLDTDNTIRYVEYVDNINSEPNFEAAIAAAKAL 163
                            |       10        20        30        40        50        60        70        80 |      90       100 |     110       120       130       140       150       160   
                            1-MSE                                                                           82-MSE             102-MSE                                                         

   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 1PSQ)

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPX_STRP2 | Q04JB8)
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_STRPN | P0C2J8)
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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