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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FUNGAL PEROXIDASE FROM ARTHROMYCES RAMOSUS AT 1.9 ANGSTROMS RESOLUTION: STRUCTURAL COMPARISONS WITH THE LIGNIN AND CYTOCHROME C PEROXIDASES
 
Authors :  N. Kunishima, K. Fukuyama
Date :  18 Jun 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase(Donor:H2O2 Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kunishima, K. Fukuyama, H. Matsubara, H. Hatanaka, Y. Shibano, T. Amachi
Crystal Structure Of The Fungal Peroxidase From Arthromyces Ramosus At 1. 9 A Resolution. Structural Comparisons With Th Lignin And Cytochrome C Peroxidases.
J. Mol. Biol. V. 235 331 1994
PubMed-ID: 8289254  |  Reference-DOI: 10.1016/S0022-2836(05)80037-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Engineered: YES
    Organism Common: PENICILLIUM VITALE
    Organism Scientific: PENICILLIUM JANTHINELLUM
    Organism Taxid: 5079

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:143 , SER A:144 , NAG A:349 , HOH A:378 , HOH A:475 , HOH A:476BINDING SITE FOR RESIDUE NAG A 348
2AC2SOFTWAREALA A:82 , ARG A:104 , NAG A:348 , HOH A:497BINDING SITE FOR RESIDUE NAG A 349
3AC3SOFTWAREASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:424 , HOH A:425BINDING SITE FOR RESIDUE CA A 346
4AC4SOFTWARESER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209BINDING SITE FOR RESIDUE CA A 347
5AC5SOFTWAREARG A:48 , LEU A:51 , ARG A:52 , PHE A:55 , PRO A:154 , GLY A:155 , LEU A:181 , ALA A:183 , HIS A:184 , LEU A:186 , ALA A:187 , SER A:188 , GLN A:189 , GLU A:190 , GLY A:191 , LEU A:192 , MET A:243 , SER A:245 , HOH A:360 , HOH A:361 , HOH A:394 , HOH A:415 , HOH A:416BINDING SITE FOR RESIDUE HEM A 345
6CA1unknownCA A:346 , ASP A:57 , GLY A:75 , ASP A:77 , SER A:79 , HOH A:424 , HOH A:425NULL
7CA2unknownCA A:347 , SER A:185 , ASP A:202 , THR A:204 , VAL A:207 , ASP A:209NULL
8GL1unknownNAG A:348 , NAG A:349 , ASN A:143NULL

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:24
2A:23 -A:293
3A:43 -A:129
4A:257 -A:322

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.PER_ARTRA67-78  1A:47-58
2PEROXIDASE_4PS50873 Plant heme peroxidase family profile.PER_ARTRA70-317  1A:50-297
3PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.PER_ARTRA196-206  1A:176-186

(-) Exons   (0, 0)

(no "Exon" information available for 1ARP)

(-) 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:336
 aligned with PER_ARTRA | P28313 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:336
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358      
            PER_ARTRA    29 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 364
               SCOP domains d1arpa_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -----------1arpA01 A:20-153,A:277-304  [code=1.10.520.10, no name defined]                                                                       1arpA02 A:154-276,A:305-344 Peroxidase, domain 2                                                                           1arpA01 A:20-153,A:277-304  1arpA02 A:154-276,A:305-344              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ................hhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhh..............hhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee..........hhhhhh...............ee........-hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh.........ee...............ee.....................ee............ Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ee----------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------------PEROXIDASE_-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------PEROXIDASE_4  PDB: A:50-297 UniProt: 70-317                                                                                                                                                                                                             ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1arp A   9 SVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1ARP)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PER_ARTRA | P28313)
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.

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  1arp
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  PER_ARTRA | P28313
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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
        PER_ARTRA | P28313: 1aru 1arv 1arw 1arx 1ary 1c8i 1ck6 1gza 1gzb 1hsr 2e39 2e3a 2e3b

(-) Related Entries Specified in the PDB File

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