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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF RAT HBP23/PEROXIREDOXIN I, CYS52SER MUTANT
 
Authors :  T. Matsumura, K. Okamoto, T. Nishino, Y. Abe
Date :  25 Sep 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Peroxiredoxin, 2-Cys Type Peroxiredoxin, Decamer, Thiol- Specific Antioxidant Protein, Hbp23, Cytoplasm, Oxidoreductase, Peroxidase, Phosphorylation, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Matsumura, K. Okamoto, S. Iwahara, H. Hori, Y. Takahashi, T. Nishino, Y. Abe
Dimer-Oligomer Interconversion Of Wild-Type And Mutant Rat 2-Cys Peroxiredoxin: Disulfide Formation At Dimer-Dimer Interfaces Is Not Essential For Decamerization
J. Biol. Chem. V. 283 284 2008
PubMed-ID: 17974571  |  Reference-DOI: 10.1074/JBC.M705753200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIREDOXIN-1
    Chains: A, B, C, D, E, F, G, H, I, J
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PRDX1, TDPX2
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: THIOREDOXIN PEROXIDASE 2, THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE 2, HEME-BINDING 23 KDA PROTEIN, HBP23

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z9S)

(-) Sites  (0, 0)

(no "Site" information available for 2Z9S)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:83 -C:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z9S)

(-) PROSITE Motifs  (1, 10)

Asymmetric/Biological Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX1_RAT6-165
 
 
 
 
 
 
 
 
 		  10A:6-165
B:6-165
C:6-165
D:6-165
E:6-165
F:6-165
G:6-165
H:6-165
I:6-165
J:6-165

(-) Exons   (5, 50)

Asymmetric/Biological Unit (5, 50)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000231321ENSRNOE00000164803chr5:136975761-13697582161PRDX1_RAT-00--
1.2ENSRNOT000000231322ENSRNOE00000164845chr5:136977666-136977782117PRDX1_RAT1-363610A:3-36
B:3-36
C:3-36
D:3-36
E:3-36
F:3-36
G:3-36
H:3-36
I:3-36
J:3-36		34
34
34
34
34
34
34
34
34
34
1.3ENSRNOT000000231323ENSRNOE00000164920chr5:136982758-136982911154PRDX1_RAT36-875210A:36-87
B:36-87
C:36-87
D:36-87
E:36-87
F:36-87
G:36-87
H:36-87
I:36-87
J:36-87		52
52
52
52
52
52
52
52
52
52
1.4ENSRNOT000000231324ENSRNOE00000164960chr5:136983328-136983450123PRDX1_RAT87-1284210A:87-128
B:87-128
C:87-128
D:87-128
E:87-128
F:87-128
G:87-128
H:87-128
I:87-128
J:87-128		42
42
42
42
42
42
42
42
42
42
1.5ENSRNOT000000231325ENSRNOE00000165006chr5:136984963-136985093131PRDX1_RAT128-1724510A:128-172
B:128-172
C:128-172
D:128-172
E:128-172
F:128-172
G:128-172
H:128-172
I:128-172
J:128-172		45
45
45
45
45
45
45
45
45
45
1.6ENSRNOT000000231326ENSRNOE00000165051chr5:136991313-136991633321PRDX1_RAT172-1992810A:172-199
B:172-199
C:172-199
D:172-199
E:172-199
F:172-199
G:172-199
H:172-199
I:172-199
J:172-199		28
28
28
28
28
28
28
28
28
28

(-) 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:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sa_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sA00 A:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.......eee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhhh..hhhhh...eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: A:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: A:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: A:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: A:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: A:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s A   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain B from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sb_ B: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sB00 B:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhhh..........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: B:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: B:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: B:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: B:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: B:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s B   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain C from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sc_ C: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sC00 C:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh........eee...hhhhhhh...hhhhh...eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: C:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: C:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: C:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: C:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: C:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s C   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain D from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sd_ D: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sD00 D:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: D:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: D:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: D:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: D:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: D:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s D   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain E from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9se_ E: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sE00 E:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: E:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: E:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: E:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: E:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: E:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: E:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s E   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain F from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sf_ F: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sF00 F:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: F:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: F:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: F:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: F:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: F:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: F:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s F   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain G from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sg_ G: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sG00 G:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: G:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: G:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: G:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: G:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: G:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: G:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s G   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain H from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sh_ H: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sH00 H:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: H:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: H:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: H:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: H:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: H:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: H:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s H   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain I from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9si_ I: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sI00 I:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: I:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: I:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: I:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: I:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: I:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: I:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s I   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       


Chain J from PDB  Type:PROTEIN  Length:197
 aligned with PRDX1_RAT | Q63716 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
            PRDX1_RAT     3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
               SCOP domains d2z9sj_ J: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 2z9sJ00 J:3-199 Glutaredoxin                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee...eeeeee.hhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..eehhhhee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh....................hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---THIOREDOXIN_2  PDB: J:6-165 UniProt: 6-165                                                                                                                      ---------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: J:3-36 [INCOMPLETE]--------------------------------------------------Exon 1.4  PDB: J:87-128 UniProt: 87-128   -------------------------------------------Exon 1.6  PDB: J:172-199     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.3  PDB: J:36-87 UniProt: 36-87               ----------------------------------------Exon 1.5  PDB: J:128-172 UniProt: 128-172    --------------------------- Transcript 1 (2)
                 2z9s J   3 SGNAKIGHPAPSFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVSPTEIIAFSDRAEEFKKLNCQVIGASVDSHFCHLAWINTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITINDLPVGRSVDEILRLVQAFQFTDKHGEVCPAGWKPGSDTIKPDVNKSKEYFSKQK 199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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, 10)

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

(-) CATH Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Glutaredoxin (620)
(-)
Homologous Superfamily: Glutaredoxin (617)
(-)
Norway rat (Rattus norvegicus) (10)
1a2z9sA00A:3-199
1b2z9sB00B:3-199
1c2z9sC00C:3-199
1d2z9sD00D:3-199
1e2z9sE00E:3-199
1f2z9sF00F:3-199
1g2z9sG00G:3-199
1h2z9sH00H:3-199
1i2z9sI00I:3-199
1j2z9sJ00J:3-199

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z9S)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (PRDX1_RAT | Q63716)
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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    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.
    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: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:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005719    nuclear euchromatin    The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX1_RAT | Q63716: 1qq2

(-) Related Entries Specified in the PDB File

1qq2 THE STRUCTURE OF ANOTHER HBP23 MUTANT