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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S-ACETANILIDE MODIFIED FORM OF C165S AHPC
 
Authors :  P. A. Karplus, A. Hall
Date :  24 Sep 08  (Deposition) - 03 Mar 09  (Release) - 03 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Oxidoreductase, Ahpc, Peroxiredoxin, Antioxidant, Peroxidase, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Nelson, D. Parsonage, A. Hall, P. A. Karplus, L. B. Poole
Cysteine Pk(A) Values For The Bacterial Peroxiredoxin Ahpc
Biochemistry V. 47 12860 2008
PubMed-ID: 18986167  |  Reference-DOI: 10.1021/BI801718D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT C
    Chains: A, B, C, D, E
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAC1
    Expression System Strain: TA4315
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AHPC
    Mutation: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: PEROXIREDOXIN, THIOREDOXIN PEROXIDASE, ALKYL HYDROPEROXIDE REDUCTASE PROTEIN C22

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3EMP)

(-) Sites  (0, 0)

(no "Site" information available for 3EMP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EMP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EMP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EMP)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.AHPC_SALTY2-157
 
 
 		  4B:1-156
C:1-156
D:1-156
E:1-156
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.AHPC_SALTY2-157
 
 
 		  8B:1-156
C:1-156
D:1-156
E:1-156

(-) Exons   (0, 0)

(no "Exon" information available for 3EMP)

(-) 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:161
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:161
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 
           AHPC_SALTY     3 LINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 163
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3empA00 A:2-162 Glutaredoxin                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..eeeeeehhhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhhh...eeee...hhhhhhh............eeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: - UniProt: 2-157                                                                                                                       ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3emp A   2 LINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3empB00 B:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhhhh..eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: B:1-156 UniProt: 2-157                                                                                                                  ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3emp B   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 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 AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3empC00 C:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh.hhhhh..eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: C:1-156 UniProt: 2-157                                                                                                                  ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3emp C   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain D from PDB  Type:PROTEIN  Length:162
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3empD00 D:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeehhhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: D:1-156 UniProt: 2-157                                                                                                                  ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3emp D   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain E from PDB  Type:PROTEIN  Length:162
 aligned with AHPC_SALTY | P0A251 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
           AHPC_SALTY     2 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3empE00 E:1-162 Glutaredoxin                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee..eeeeee.hhh...eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhhh...eeee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE THIOREDOXIN_2  PDB: E:1-156 UniProt: 2-157                                                                                                                  ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3emp E   1 SLINTKIKPFKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYSVSTDTHFTHKAWHSSSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDPQGIIQAIEVTAEGIGRDASDLLRKIKAAQYVAAHPG 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3EMP)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EMP)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (AHPC_SALTY | P0A251)
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: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.
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.

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  1.11.1.15
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 Related Entries

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

UniProtKB/Swiss-Prot
        AHPC_SALTY | P0A251: 1n8j 1yep 1yex 1yf0 1yf1 4ma9 4mab 4xra 4xrd 4xs1 4xs4 4xs6 4xs8 4xts

(-) Related Entries Specified in the PDB File

1n8j MOLECULAR REPLACEMENT SEARCH MODEL
1yf1 MOLECULAR REPLACEMENT SEARCH MODEL