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(-) Description

Title :  PRX D (TYPE II) FROM POPULUS TREMULA
 
Authors :  A. Echalier, X. Trivelli, C. Corbier, N. Rouhier, O. Walker, P. Tsan, J. P. Jacquot, I. Krimm, J. M. Lancelin
Date :  16 Jun 04  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Peroxiredoxin, Oligomer, Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Echalier, X. Trivelli, C. Corbier, N. Rouhier, O. Walker, P. Tsan, J. P. Jacquot, A. Aubry, I. Krimm, J. M. Lancelin
Crystal Structure And Solution Nmr Dynamics Of A D (Type Ii) Peroxiredoxin Glutaredoxin And Thioredoxin Dependent: A New Insight Into The Peroxiredoxin Oligomerism
Biochemistry V. 44 1755 2005
PubMed-ID: 15697201  |  Reference-DOI: 10.1021/BI048226S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIREDOXIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET3D
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificPOPULUS TRICHOCARPA
    Organism Taxid3694
    SynonymPRX D (TYPE II)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:49 , THR A:50 , LYS A:121 , HOH A:1317 , HOH A:1371 , HOH A:1439BINDING SITE FOR RESIDUE SO4 A 1248
2AC2SOFTWAREPRO B:49 , THR B:50 , HOH B:1366BINDING SITE FOR RESIDUE SO4 B 1249

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TP9)

(-) Exons   (0, 0)

(no "Exon" information available for 1TP9)

(-) 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:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9a1 A:1-162 Plant peroxiredoxin                                                                                                                                SCOP domains
               CATH domains 1tp9A00 A:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 A   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain A from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9a1 A:1-162 Plant peroxiredoxin                                                                                                                                SCOP domains
               CATH domains 1tp9A00 A:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 A   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9B00 B:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 B   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9B00 B:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eeee.....eeee..eeeeee..eeeeeee.........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 B   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         A9PCL4_POPTR     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKDL 162
               SCOP domains d1tp9c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9C00 C:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh.......eeeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 C   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8S3L0_9ROSI     1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
               SCOP domains d1tp9c_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains 1tp9C00 C:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee.....eeeeehhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh.......eeeee...hhhhhhh..eee.......eee..eeeeee..eeeeeee.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tp9 C   1 MAPIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKDL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with A9PCL4_POPTR | A9PCL4 from UniProtKB/TrEMBL  Length:162

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         A9PCL4_POPTR     2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELNLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSADDILKD 161
               SCOP domains d1tp9d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains 1tp9D00 D:2-161 Glutaredoxin                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp9 D   2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:160
 aligned with Q8S3L0_9ROSI | Q8S3L0 from UniProtKB/TrEMBL  Length:162

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         Q8S3L0_9ROSI     2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
               SCOP domains d1tp9d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains 1tp9D00 D:2-161 Glutaredoxin                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeeehhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh......eeeee...hhhhhhh..eee.hhhh..eee..eeeeee..eeeeeee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tp9 D   2 APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGVTEILCISVNDPFVMKAWAKSYPENKHVKFLADGSATYTHALGLELDLQEKGLGTRSRRFALLVDDLKVKAANIEGGGEFTVSSAEDILKD 161
                                    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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TP9)

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A9PCL4_POPTR | A9PCL4)
molecular function
    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.
biological process
    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.

Chain A,B,C,D   (Q8S3L0_9ROSI | Q8S3L0)
molecular function
    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.
biological process
    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.

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