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(-) Description

Title :  DYP-TYPE PEROXIDASE OF AURICULARIA AURICULA-JUDAE (AAUDYPI) CRYSTALLIZED AT PH 6.5
 
Authors :  E. Strittmatter, K. Piontek, D. A. Plattner
Date :  27 Jan 15  (Deposition) - 09 Mar 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Dye-Decolorizing Peroxidase, Dyp, Fungal, Heme, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Strittmatter, K. Piontek, D. A. Plattner
Crystallographic Trapping Of A Covalently Modified Heme In A Dye-Decolorizing Peroxidase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DYE-DECOLORIZING PEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.19
    Fragment: DYP-TYPE PEROXIDASE DOMAIN, RESIDUES 64-509
    Organism Common: EAR FUNGUS
    Organism Scientific: AURICULARIA AURICULA-JUDAE
    Organism Taxid: 29892
    Other Details: INCLUDING THE TWO PROTEIN CHAINS, THE CO- FACTOR DELTA-MESO NITROHEME, CARBOHYDRATE MOLECULES, CACODYLATE, FORMATE, GLYCEROL, NITRITE, AND WATER MOLECULES.
    Other Details - Source: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSM 11326
    Strain: SXM9-C021

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 31)

Asymmetric Unit (7, 31)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CAC2Ligand/IonCACODYLATE ION
3FMT4Ligand/IonFORMIC ACID
4GOA1Ligand/IonGLYCOLIC ACID
5GOL15Ligand/IonGLYCEROL
6HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (7, 19)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CAC1Ligand/IonCACODYLATE ION
3FMT2Ligand/IonFORMIC ACID
4GOA1Ligand/IonGLYCOLIC ACID
5GOL9Ligand/IonGLYCEROL
6HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (5, 12)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2CAC1Ligand/IonCACODYLATE ION
3FMT2Ligand/IonFORMIC ACID
4GOA-1Ligand/IonGLYCOLIC ACID
5GOL6Ligand/IonGLYCEROL
6HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:162 , PHE A:166 , LEU A:167 , ASP A:168 , GLY A:169 , ILE A:170 , ALA A:171 , GLN A:221 , ARG A:255 , HIS A:304 , ILE A:305 , THR A:308 , ARG A:309 , ARG A:311 , ARG A:332 , LEU A:357 , PHE A:359 , PHE A:370 , ILE A:398 , FMT A:1456 , HOH A:2253 , HOH A:2270 , HOH A:2277 , HOH A:2386BINDING SITE FOR RESIDUE HEM A1449
02AC2SOFTWAREGLU B:162 , PHE B:166 , LEU B:167 , ASP B:168 , GLY B:169 , ILE B:170 , ALA B:171 , LEU B:219 , GLN B:221 , ARG B:255 , HIS B:304 , THR B:308 , ARG B:309 , ARG B:311 , ARG B:332 , LEU B:357 , PHE B:359 , PHE B:370 , ILE B:398 , FMT B:1460 , HOH B:2186 , HOH B:2201 , HOH B:2207 , HOH B:2276BINDING SITE FOR RESIDUE HEM B1449
03AC3SOFTWARESER A:286 , HIS A:287 , ALA A:288 , HOH A:2397BINDING SITE FOR RESIDUE CAC A1455
04AC4SOFTWAREHIS B:287 , ALA B:288BINDING SITE FOR RESIDUE CAC B1452
05AC5SOFTWAREARG A:332 , LEU A:357 , PHE A:359 , HEM A:1449 , GOA A:1459 , HOH A:2317BINDING SITE FOR RESIDUE FMT A1456
06AC6SOFTWAREARG B:154 , GLU B:158 , MET B:163 , HOH B:2190BINDING SITE FOR RESIDUE FMT B1453
07AC7SOFTWARELYS A:99 , HOH A:2363 , HOH A:2366BINDING SITE FOR RESIDUE FMT A1457
08AC8SOFTWARESER A:3 , LEU A:4 , ASN A:5 , ILE A:9 , GLY A:210 , HOH A:2009 , HOH A:2206BINDING SITE FOR RESIDUE GOL A1458
09AC9SOFTWAREASP A:168 , GLY A:169 , GLN A:172 , ARG A:332 , SER A:333 , GLY A:334 , FMT A:1456BINDING SITE FOR RESIDUE GOA A1459
10BC1SOFTWAREPRO B:385 , GLY B:386 , LYS B:387 , ALA B:390 , HOH B:2257BINDING SITE FOR RESIDUE GOL B1454
11BC2SOFTWAREPRO B:235 , LEU B:247 , PRO B:413 , SER B:414 , HOH B:2178BINDING SITE FOR RESIDUE GOL B1455
12BC3SOFTWAREASP A:129 , GLN A:130 , HOH A:2142 , HOH A:2398 , HOH A:2399 , HOH A:2400 , SER B:152 , PRO B:339 , GOL B:1457BINDING SITE FOR RESIDUE GOL A1460
13BC4SOFTWARELEU B:149 , TYR B:337 , HOH B:2120 , HOH B:2244BINDING SITE FOR RESIDUE GOL B1456
14BC5SOFTWAREGOL A:1460 , SER B:150 , SER B:152 , TYR B:337 , GLY B:338 , HOH B:2126BINDING SITE FOR RESIDUE GOL B1457
15BC6SOFTWAREASP A:42 , VAL A:46 , GLN A:131 , SER A:134 , ILE A:135 , THR A:138 , HOH A:2149BINDING SITE FOR RESIDUE GOL A1461
16BC7SOFTWAREGLY A:169 , GLY A:274 , ALA A:275 , ASN A:280 , HOH A:2184BINDING SITE FOR RESIDUE GOL A1462
17BC8SOFTWAREGLY A:196 , ALA A:197 , ASN A:199 , ASP A:200 , GOL A:1464 , GOL A:1465BINDING SITE FOR RESIDUE GOL A1463
18BC9SOFTWAREPRO A:201 , GOL A:1463 , HOH A:2209 , ARG B:445 , ALA B:448BINDING SITE FOR RESIDUE GOL A1464
19CC1SOFTWAREGLY A:196 , GOL A:1463 , SER B:206 , VAL B:209 , HOH B:2168BINDING SITE FOR RESIDUE GOL A1465
20CC2SOFTWARESER A:206 , TRP A:207 , VAL A:209 , HOH A:2213 , HOH A:2214 , GOL B:1459BINDING SITE FOR RESIDUE GOL A1466
21CC3SOFTWAREASN A:227 , LEU A:231 , GLN A:242 , ALA A:245 , ASP A:246 , HOH A:2245 , HOH A:2403BINDING SITE FOR RESIDUE GOL A1467
22CC4SOFTWAREASP B:42 , GLN B:131 , SER B:134 , HOH B:2036BINDING SITE FOR RESIDUE GOL B1458
23CC5SOFTWAREGOL A:1466 , GLY B:196 , ALA B:197 , THR B:198 , ASN B:199 , ASP B:200BINDING SITE FOR RESIDUE GOL B1459
24CC6SOFTWAREARG B:332 , LEU B:357 , PHE B:359 , HEM B:1449 , HOH B:2235 , HOH B:2236BINDING SITE FOR RESIDUE FMT B1460
25CC7SOFTWAREGLN A:278 , ASN A:282 , PRO A:320 , HOH A:2272 , HOH A:2387 , HOH A:2388 , HOH A:2390BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1450 THROUGH BMA A1452 BOUND TO ASN A 282
26CC8SOFTWARELYS A:228 , ASP A:232 , ALA A:347 , ASN A:349 , HOH A:2391BINDING SITE FOR MONO-SACCHARIDE NAG A1453 BOUND TO ASN A 349
27CC9SOFTWAREASN A:415 , SER A:417 , ALA A:418 , HOH A:2377 , HOH A:2392 , HOH A:2394 , HOH A:2395 , HOH A:2396BINDING SITE FOR MONO-SACCHARIDE NAG A1454 BOUND TO ASN A 415
28DC1SOFTWAREGLN B:278 , ARG B:279 , ASN B:282 , PRO B:320 , HOH B:2203BINDING SITE FOR MONO-SACCHARIDE NAG B1451 BOUND TO ASN B 282
29DC2SOFTWAREASP B:232 , ALA B:347 , ASN B:349 , HOH B:2174BINDING SITE FOR MONO-SACCHARIDE NAG B1450 BOUND TO ASN B 349

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AG0)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Pro A:320 -Pro A:321
2Phe A:383 -Pro A:384
3Thr A:388 -Pro A:389
4Ala B:288 -Gly B:289
5Pro B:320 -Pro B:321
6Phe B:383 -Pro B:384
7Thr B:388 -Pro B:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AG0)

(-) Exons   (0, 0)

(no "Exon" information available for 5AG0)

(-) 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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhhh............................eeee.........eeee...eeeeeeeeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ag0 A   3 SLNTDDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 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      


Chain B from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeehhhhhhhh.......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
                 5ag0 B   3 SLNTDDIQGDILVGMHKQKQLFYFFAINDPATFKTHLASDIAPVVASVTQLSNVATQPLVALNIAFSNTGLLALGVTDNLGDSLFANGQAKDATSFKESTSSWVPQFAGTGIHGVIILASDTTDLIDQQVASIESTFGSSISKLYSLSASIRPGNEAGHEMFGFLDGIAQPAINGFNTPLPGQNIVDAGVIITGATNDPITRPSWAVGGSFLAFRQLEQLVPEFNKYLLDNAPAGSGSLQARADLLGARMVGRWKSGAPIDLTPTADDPALGADAQRNNNFTYSHAGFDLGSDQSHCPFSAHIRKTRPRADLGGSLTPPNLSAGANSIMRSGIPYGPEVTSAESASNTTTQERGLAFVAYQAQLSQGFHFLQQTWADNANFPPGKTPATVGLDPIIGQNNGQPRVVNGLLPSNSSASLSIPQFVVSHGGEYFFSPPISAIGGRLSA 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
   Legend:   → Mismatch (orange background)
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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 5AG0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AG0)

(-) Gene Ontology  (6, 6)

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        I2DBY1_AURAJ | I2DBY1: 4au9 4uzi 4w7j 4w7k 4w7l 4w7m 4w7n 4w7o 5ag1 5ikd 5ikg

(-) Related Entries Specified in the PDB File

5ag1 DYP-TYPE PEROXIDASE OF AURICULARIA AURICULA-JUDAE ( AAUDYPI) WITH MESO-NITRATED HEME