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(-) Description

Title :  RECOMBINANT HORSERADISH PEROXIDASE C1A PHE221MET
 
Authors :  A. Henriksen, N. Brissett, M. Gajhede
Date :  25 Mar 02  (Deposition) - 28 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Henriksen, N. Brissett, K. Meno, O. Mirza, M. Gajhede
Hrpc Heme Crevice Architecture
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDASE C1A
    Chains: A
    EC Number: 1.11.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: HORSERADISH
    Organism Scientific: ARMORACIA RUSTICANA
    Organism Taxid: 3704
    Other Details: SYNTHETIC GENE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOICACID
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NA1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:2112BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWARETHR A:171 , ASP A:222 , THR A:225 , ILE A:228 , ASP A:230BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREHOH A:2176 , HOH A:2373 , HOH A:2374 , HOH A:2378 , HOH A:2381BINDING SITE FOR RESIDUE NA A 503
4AC4SOFTWAREARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , PRO A:139 , ALA A:140 , PRO A:141 , LEU A:166 , GLY A:169 , HIS A:170 , PHE A:172 , GLY A:173 , LYS A:174 , ASN A:175 , GLN A:176 , PHE A:179 , MET A:221 , SER A:246 , HOH A:2252 , HOH A:2324 , HOH A:2407 , HOH A:2408 , HOH A:2409BINDING SITE FOR RESIDUE HEM A 350
5AC5SOFTWAREASN A:16 , ASP A:20 , ALA A:90 , ARG A:224 , THR A:225BINDING SITE FOR RESIDUE FER A 701

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:91
2A:11 -A:91
3A:44 -A:49
4A:97 -A:301
5A:177 -A:209

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_4PS50873 Plant heme peroxidase family profile.PER1A_ARMRU31-335  1A:1-305
2PEROXIDASE_2PS00436 Peroxidases active site signature.PER1A_ARMRU63-74  1A:33-44
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.PER1A_ARMRU192-202  1A:162-172

(-) Exons   (0, 0)

(no "Exon" information available for 1GWT)

(-) 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:308
 aligned with PER1A_ARMRU | P00433 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:308
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329        
          PER1A_ARMRU    30 AQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDFDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 337
               SCOP domains d1gwta_ A: Plant peroxidase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --1gwtA01 A:2-138,A:285-305  [code=1.10.520.10, no name defined]                                                                           1gwtA02 A:139-284 Peroxidase, domain 2                                                                                                            1gwtA01              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.eee...hhhhhhhhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PEROXIDASE_4  PDB: A:1-305 UniProt: 31-335                                                                                                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gwt A   0 MQLTPTFYDNSCPNVSNIVRDTIVNELRSDPRIAASILRLHFHDCFVNGCDASILLDNTTSFRTEKDAFGNANSARGFPVIDRMKAAVESACPRTVSCADLLTIAAQQSVTLAGGPSWRVPLGRRDSLQAFLDLANANLPAPFFTLPQLKDSFRNVGLNRSSDLVALSGGHTFGKNQCRFIMDRLYNFSNTGLPDPTLNTTYLQTLRGLCPLNGNLSALVDMDLRTPTIFDNKYYVNLEEQKGLIQSDQELFSSPNATDTIPLVRSFANSTQTFFNAFVEAMDRMGNITPLTGTQGQIRLNCRVVNSN 307
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PER1A_ARMRU | P00433)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  1gwt
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  PER1A_ARMRU | P00433
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  1.11.1.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        PER1A_ARMRU | P00433: 1atj 1gw2 1gwo 1gwu 1gx2 1h55 1h57 1h58 1h5a 1h5c 1h5d 1h5e 1h5f 1h5g 1h5h 1h5i 1h5j 1h5k 1h5l 1h5m 1hch 1kzm 1w4w 1w4y 2atj 2ylj 3atj 4atj 6atj 7atj

(-) Related Entries Specified in the PDB File

1atj RECOMBINANT HORSERADISH PEROXIDASE C1A
1gw2 RECOMBINANT HORSERADISH PEROXIDASE C1A THR171SER IN COMPLEX WITH FERULIC ACID
1gwo RECOMBINANT HORSERADISH PEROXIDASE C1A ALA140GLN
1gwu RECOMBINANT HORSERADISH PEROXIDASE C1A ALA140GLY
1gx2 RECOMBINANT HORSERADISH PEROXIDASE PHE179SER COMPLEX WITH BENZHYDROXAMIC ACID
1h55 STRUCTURE OF HORSERADISH PEROXIDASE C1A COMPOUND II
1h57 STRUCTURE OF HORSERADISH PEROXIDASE C1A COMPOUND III
1h58 STRUCTURE OF FERROUS HORSERADISH PEROXIDASE C1A
1h5a STRUCTURE OF FERRIC HORSERADISH PEROXIDASE C1A IN COMPLEX WITH ACETATE
1h5c X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (100-200% DOSE)
1h5d X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-11% DOSE)
1h5e X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (11-22% DOSE)
1h5f X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (22-33% DOSE)
1h5g X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (33-44% DOSE)
1h5h X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (44-56% DOSE)
1h5i X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (56-67% DOSE)
1h5j X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (67-78% DOSE)
1h5k X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (78-89% DOSE)
1h5l X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (89-100% DOSE)
1h5m X-RAY INDUCED REDUCTION OF HORSERADISH PEROXIDASE C1A COMPOUND III (0-100% DOSE)
1hch HORSERADISH PEROXIDASE COMPOUND I
1kzm DISTAL HEME POCKET MUTANT (R38S/H42E) OF RECOMBINANTHORSERADISH PEROXIDASE C (HRP C).
2atj RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID
3atj HEME LIGAND MUTANT OF RECOMBINANT HORSERADISH PEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
4atj DISTAL HEME POCKET MUTANT (H42E) OF RECOMBINANT HORSERADISHPEROXIDASE IN COMPLEX WITH BENZHYDROXAMIC ACID
6atj RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID
7atj RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID