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(-) Description

Title :  ARABIDOPSIS THALIANA PEROXIDASE A2
 
Authors :  A. Henriksen
Date :  18 May 99  (Deposition) - 15 Nov 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Ostergaard, K. Teilum, O. Mirza, O. Mattsson, M. Petersen, K. G. Welinder, J. Mundy, M. Gajhede, A. Henriksen
Arabidopsis Atp A2 Peroxidase. Expression And High-Resolution Structure Of A Plant Peroxidase With Implications For Lignification.
Plant Mol. Biol. V. 44 231 2000
PubMed-ID: 11117266  |  Reference-DOI: 10.1023/A:1006442618860
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATP A2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:591BINDING SITE FOR RESIDUE CA A 307
2AC2SOFTWARETHR A:170 , ASP A:221 , THR A:224 , ALA A:227 , ASP A:229BINDING SITE FOR RESIDUE CA A 308
3AC3SOFTWAREHOH A:483 , HOH A:563 , HOH A:748 , HOH A:749 , HOH A:762BINDING SITE FOR RESIDUE MG A 309
4AC4SOFTWAREARG A:31 , ALA A:34 , SER A:35 , ARG A:38 , PHE A:41 , SER A:73 , PRO A:139 , SER A:140 , PRO A:141 , PHE A:152 , LEU A:162 , LEU A:165 , SER A:166 , ALA A:168 , HIS A:169 , GLY A:172 , ARG A:173 , ALA A:174 , ARG A:175 , SER A:245 , HOH A:353 , HOH A:356 , HOH A:605 , HOH A:633BINDING SITE FOR RESIDUE HEM A 306

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:91
2A:44 -A:49
3A:97 -A:299
4A:176 -A:208

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PA2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PA2)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_4PS50873 Plant heme peroxidase family profile.PER53_ARATH31-333  1A:1-303
2PEROXIDASE_2PS00436 Peroxidases active site signature.PER53_ARATH63-74  1A:33-44
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.PER53_ARATH191-201  1A:161-171

(-) Exons   (0, 0)

(no "Exon" information available for 1PA2)

(-) 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:306
 aligned with PER53_ARATH | Q42578 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:306
                                    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      
          PER53_ARATH    30 AQLNATFYSGTCPNASAIVRSTIQQALQSDTRIGASLIRLHFHDCFVNGCDASILLDDTGSIQSEKNAGPNVNSARGFNVVDNIKTALENACPGVVSCSDVLALASEASVSLAGGPSWTVLLGRRDSLTANLAGANSSIPSPIESLSNITFKFSAVGLNTNDLVALSGAHTFGRARCGVFNNRLFNFSGTGNPDPTLNSTLLSTLQQLCPQNGSASTITNLDLSTPDAFDNNYFANLQSNDGLLQSDQELFSTTGSSTIAIVTSFASNQTLFFQAFAQSMINMGNISPLTGSNGEIRLDCKKVNGS 335
               SCOP domains d1pa2a_ A: Plant peroxidase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --1pa2A01 A:2-138,A:283-303  [code=1.10.520.10, no name defined]                                                                           1pa2A02 A:139-282 Peroxidase, domain 2                                                                                                          1pa2A01              -- CATH domains
               Pfam domains ------------------peroxidase-1pa2A01 A:18-267                                                                                                                                                                                                                               -------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhh.eee.hhhhhhh.hhhhh.......hhhhhhhhhhhh........eee..........hhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -PEROXIDASE_4  PDB: A:1-303 UniProt: 31-333                                                                                                                                                                                                                                                                     -- PROSITE (1)
                PROSITE (2) ---------------------------------PEROXIDASE_2--------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pa2 A   0 MQLNATFYSGTCPNASAIVRSTIQQALQSDTRIGASLIRLHFHDCFVNGCDASILLDDTGSIQSEKNAGPNVNSARGFNVVDNIKTALENACPGVVSCSDVLALASEASVSLAGGPSWTVLLGRRDSLTANLAGANSSIPSPIESLSNITFKFSAVGLNTNDLVALSGAHTFGRARCGVFNNRLFNFSGTGNPDPTLNSTLLSTLQQLCPQNGSASTITNLDLSTPDAFDNNYFANLQSNDGLLQSDQELFSTTGSSTIAIVTSFASNQTLFFQAFAQSMINMGNISPLTGSNGEIRLDCKKVNGS 305
                                     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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: peroxidase] (92)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PER53_ARATH | Q42578)
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:0002215    defense response to nematode    A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0009908    flower development    The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PER53_ARATH | Q42578: 1qo4

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