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(-) Description

Title :  CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE
 
Authors :  F. J. Medrano, A. Romero
Date :  22 Aug 14  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Decolorizing Peroxidase (Dyp), Oxidoreductase, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Linde, R. Pogni, M. Canellas, F. Lucas, V. Guallar, M. C. Baratto, A. Sinicropi, V. Saez-Jimenez, C. Coscolin, A. Romero, F. J. Medrano, F. J. Ruiz-Duenas, A. T. Martinez
Catalytic Surface Radical In Dye-Decolorizing Peroxidase: A Computational, Spectroscopic And Site-Directed Mutagenesis Study.
Biochem. J. V. 466 253 2015
PubMed-ID: 25495127  |  Reference-DOI: 10.1042/BJ20141211

(-) Compounds

Molecule 1 - DYE-DECOLORIZING PEROXIDASE
    Chains: A, B, C, D
    EC Number: 1.11.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 62-509
    Gene: DYP1
    Mutation: YES
    Organism Common: EAR FUNGUS
    Organism Scientific: AURICULARIA AURICULA-JUDAE
    Organism Taxid: 29892

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:162 , PHE A:166 , LEU A:167 , ASP A:168 , GLY A:169 , ILE A:170 , ALA A:171 , GLN A:221 , VAL A:253 , ARG A:255 , HIS A:304 , ILE A:305 , THR A:308 , ARG A:309 , ARG A:311 , ARG A:332 , PHE A:359 , PHE A:370 , ILE A:398 , VAL A:426 , HOH A:641 , HOH A:646 , HOH A:658 , HOH A:667 , HOH A:676binding site for residue HEM A 501
2AC2SOFTWAREGLU B:162 , PHE B:166 , LEU B:167 , ASP B:168 , GLY B:169 , ILE B:170 , ALA B:171 , GLN B:221 , ARG B:255 , HIS B:304 , ILE B:305 , THR B:308 , ARG B:309 , ARG B:311 , ARG B:332 , PHE B:359 , PHE B:370 , ILE B:398 , HOH B:677 , HOH B:679 , HOH B:711 , HOH B:729 , HOH B:743binding site for residue HEM B 501
3AC3SOFTWAREGLU C:162 , PHE C:166 , LEU C:167 , ASP C:168 , GLY C:169 , ILE C:170 , ALA C:171 , GLN C:221 , ARG C:255 , HIS C:304 , ILE C:305 , THR C:308 , ARG C:309 , ARG C:311 , ARG C:332 , PHE C:359 , PHE C:370 , GLN C:374 , ILE C:398 , HOH C:669 , HOH C:674 , HOH C:685 , HOH C:705 , HOH C:753binding site for residue HEM C 501
4AC4SOFTWAREGLU D:162 , PHE D:166 , LEU D:167 , GLY D:169 , ILE D:170 , ALA D:171 , GLN D:221 , ARG D:255 , HIS D:304 , ILE D:305 , THR D:308 , ARG D:309 , ARG D:311 , ARG D:332 , PHE D:359 , PHE D:370 , GLN D:374 , ILE D:398 , HOH D:673 , HOH D:676 , HOH D:679 , HOH D:695 , HOH D:697binding site for residue HEM D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W7J)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Pro A:320 -Pro A:321
2Phe A:383 -Pro A:384
3Thr A:388 -Pro A:389
4Pro B:320 -Pro B:321
5Phe B:383 -Pro B:384
6Thr B:388 -Pro B:389
7Pro C:320 -Pro C:321
8Phe C:383 -Pro C:384
9Thr C:388 -Pro C:389
10Pro D:320 -Pro D:321
11Phe D:383 -Pro D:384
12Thr D:388 -Pro D:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W7J)

(-) Exons   (0, 0)

(no "Exon" information available for 4W7J)

(-) 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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhh.............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7j A   4 LNTIDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443     


Chain B from PDB  Type:PROTEIN  Length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhhh..........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhhh............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7j B   2 TSLNTIDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       


Chain C from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhhh............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7j C   4 LNTIDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443     


Chain D from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhh.............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7j D   3 SLNTIDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 448
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442
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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  (0, 0)

(no "SCOP Domain" information available for 4W7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W7J)

(-) Gene Ontology  (6, 6)

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  1.11.1.19
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        I2DBY1_AURAJ | I2DBY1: 4au9 4uzi 4w7k 4w7l 4w7m 4w7n 4w7o 5ag0 5ag1 5ikd 5ikg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4W7J)