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(-) Description

Title :  CRYSTAL STRUCTURE OF AAUDYP COMPLEXED WITH IMIDAZOLE
 
Authors :  E. Strittmatter, C. Liers, R. Ullrich, M. Hofrichter, K. Piontek, D. A.
Date :  05 Sep 14  (Deposition) - 14 Jan 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Peroxidase, Dyp-Type Peroxidase, Heme, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Strittmatter, K. Serrer, C. Liers, R. Ullrich, M. Hofrichter, K. Piontek, E. Schleicher, D. A. Plattner
The Toolbox Of Auricularia Auricula-Judae Dye-Decolorizing Peroxidase - Identification Of Three New Potential Substrate-Interaction Sites.
Arch. Biochem. Biophys. V. 574 75 2015
PubMed-ID: 25542606  |  Reference-DOI: 10.1016/J.ABB.2014.12.016

(-) 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 HEME, CARBOHYDRATE MOLECULES, IMIDAZOLE, HEPES, ACETATE, GLYCOLATE, OXALATE, FORMATE, 2-METHYL-2,4- PENTANEDIOLE (RACEMIC), TRIS, POTASSIUM CATIONS AND WATER MOLECULES.
    Other Details - Source: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSMZ 11326
    Strain: SXM9-C021
    Synonym: AURICULARIA AURICULA-JUDAE DYP-TYPE PEROXIDASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 36)

Asymmetric/Biological Unit (12, 36)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
4FMT1Ligand/IonFORMIC ACID
5GOA1Ligand/IonGLYCOLIC ACID
6HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7IMD4Ligand/IonIMIDAZOLE
8K2Ligand/IonPOTASSIUM ION
9MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
10MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
11NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
12OXD1Ligand/IonOXALIC ACID

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
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 , VAL A:253 , 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 , ILE A:397 , ILE A:398 , IMD A:1454 , HOH A:2203 , HOH A:2220 , HOH A:2225 , HOH A:2309BINDING SITE FOR RESIDUE HEM A1449
02AC2SOFTWAREASP A:168 , ARG A:332 , LEU A:357 , PHE A:359 , HEM A:1449BINDING SITE FOR RESIDUE IMD A1454
03AC3SOFTWAREGLU B:162 , PHE B:166 , LEU B:167 , ASP B:168 , GLY B:169 , ILE B:170 , ALA B:171 , GLN B:221 , VAL B:253 , ARG B:255 , HIS B:304 , THR B:308 , ARG B:309 , ARG B:311 , ARG B:332 , PHE B:359 , ILE B:397 , ILE B:398 , IMD B:1455 , HOH B:2137 , HOH B:2151 , HOH B:2155 , HOH B:2209BINDING SITE FOR RESIDUE HEM B1449
04AC4SOFTWAREASP B:168 , ARG B:332 , LEU B:357 , PHE B:359 , HEM B:1449 , HOH B:2176BINDING SITE FOR RESIDUE IMD B1455
05AC5SOFTWARELEU A:14 , VAL A:15 , GLY A:16 , GLN A:172 , ARG A:332 , SER A:333 , HOH A:2021BINDING SITE FOR RESIDUE IMD A1455
06AC6SOFTWARELEU B:14 , VAL B:15 , GLY B:16 , ARG B:332 , SER B:333 , HOH B:2010BINDING SITE FOR RESIDUE IMD B1456
07AC7SOFTWAREGLY A:160 , GLY A:169 , ARG A:332 , SER A:333 , GLY A:334 , HOH A:2313 , HOH A:2314BINDING SITE FOR RESIDUE MRD A1456
08AC8SOFTWAREGLY B:160 , ASP B:168 , ARG B:332 , SER B:333 , GLY B:334 , HOH B:2212BINDING SITE FOR RESIDUE MPD B1457
09AC9SOFTWARESER A:343 , ASP B:42 , VAL B:46 , GLN B:131 , SER B:134BINDING SITE FOR RESIDUE MPD B1458
10BC1SOFTWAREASN B:176 , ILE B:187 , ASP B:189BINDING SITE FOR RESIDUE MPD B1459
11BC2SOFTWARELEU A:74 , HOH A:2062 , THR B:6 , ACT B:1464 , HOH B:2213BINDING SITE FOR RESIDUE MPD B1460
12BC3SOFTWAREILE A:187 , GLN A:404 , HOH A:2292BINDING SITE FOR RESIDUE MPD A1457
13BC4SOFTWARETHR A:124 , THR A:125 , ASP A:126 , HOH A:2102 , THR B:124 , THR B:125 , ASP B:126BINDING SITE FOR RESIDUE MPD B1461
14BC5SOFTWARELYS A:99 , ASN A:401 , HOH A:2291 , HOH A:2315BINDING SITE FOR RESIDUE MPD A1458
15BC6SOFTWARELEU A:292 , ALA A:312 , GLY A:315 , GLY A:316 , LEU A:318 , HOH A:2316 , HOH A:2317BINDING SITE FOR RESIDUE FMT A1459
16BC7SOFTWARELYS B:145 , TYR B:147 , SER B:148 , HOH B:2214BINDING SITE FOR RESIDUE EPE B1462
17BC8SOFTWAREGLN A:108 , LYS A:145 , LEU A:146 , TYR A:147 , SER A:148BINDING SITE FOR RESIDUE EPE A1460
18BC9SOFTWARETYR A:25 , GLU A:136 , SER A:144 , LYS A:145BINDING SITE FOR RESIDUE ACT A1461
19CC1SOFTWARESER B:346 , ASN B:349 , HOH B:2215BINDING SITE FOR RESIDUE ACT B1463
20CC2SOFTWARELEU A:74 , MPD B:1460 , HOH B:2104BINDING SITE FOR RESIDUE ACT B1464
21CC3SOFTWAREHOH B:2102BINDING SITE FOR RESIDUE ACT B1467
22CC4SOFTWAREASP A:232 , LEU A:241 , NAG A:1452 , HOH A:2312BINDING SITE FOR RESIDUE ACT A1462
23CC5SOFTWAREASP A:42 , GLN A:131 , SER A:134BINDING SITE FOR RESIDUE ACT A1463
24CC6SOFTWARESER A:346 , ALA A:347 , ASN A:349BINDING SITE FOR RESIDUE OXD A1464
25CC7SOFTWAREASP B:84 , LEU B:366 , SER B:367 , HOH B:2054 , HOH B:2183BINDING SITE FOR RESIDUE K B1465
26CC8SOFTWAREASP A:84 , LEU A:366 , SER A:367 , HOH A:2075 , HOH A:2271BINDING SITE FOR RESIDUE K A1465
27CC9SOFTWAREGLN A:278 , ASN A:282 , PRO A:320 , HOH A:2222 , HOH A:2310 , HOH A:2311BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1450 THROUGH NAG A1451 BOUND TO ASN A 282
28DC1SOFTWARELYS A:228 , ASP A:232 , ALA A:347 , ASN A:349 , ACT A:1462BINDING SITE FOR MONO-SACCHARIDE NAG A1452 BOUND TO ASN A 349
29DC2SOFTWAREASN A:415 , SER A:417 , ALA A:418 , HOH A:2301BINDING SITE FOR MONO-SACCHARIDE NAG A1453 BOUND TO ASN A 415
30DC3SOFTWAREPRO B:183 , GLN B:278 , ASN B:282 , PRO B:320 , HOH B:2210BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1450 THROUGH BMA B1452 BOUND TO ASN B 282
31DC4SOFTWAREASP B:232 , ALA B:347 , ASN B:349BINDING SITE FOR MONO-SACCHARIDE NAG B1453 BOUND TO ASN B 349
32DC5SOFTWAREASN B:415 , SER B:417BINDING SITE FOR MONO-SACCHARIDE NAG B1454 BOUND TO ASN B 415

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Pro A:320 -Pro A:321
2Phe A:383 -Pro A:384
3Thr A:388 -Pro A:389
4Ser B:238 -Gly B:239
5Ala B:288 -Gly B:289
6Pro B:320 -Pro B:321
7Phe B:383 -Pro B:384
8Thr B:388 -Pro B:389

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UZI)

(-) 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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhh........eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhh..........eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..hhhhh..............ee...........eehhhhh...........hhhhh..eeeeeeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...............hhhhhh...........................hhhhhhhhhhhhh.........hhhhh.ee..eee....hhhhhhhh......eeeeeeee.....hhhhhhhh.............................eeee.........eeee...eeeeeeeeeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uzi 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..hhhhhh........eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhh..........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
                 4uzi 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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  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 4UZI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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        I2DBY1_AURAJ | I2DBY1: 4au9 4w7j 4w7k 4w7l 4w7m 4w7n 4w7o 5ag0 5ag1 5ikd 5ikg

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