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(-) Description

Title :  DYP2 FROM AMYCOLATOPSIS SP. ATCC 39116
 
Authors :  M. E. Brown, T. Barros, M. C. Y. Chang
Date :  11 Jul 12  (Deposition) - 24 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dye Peroxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Brown, T. Barros, M. C. Chang
Identification And Characterization Of A Multifunctional Dy Peroxidase From A Lignin-Reactive Bacterium.
Acs Chem. Biol. V. 7 2074 2012
PubMed-ID: 23054399  |  Reference-DOI: 10.1021/CB300383Y

(-) Compounds

Molecule 1 - DYP2
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-T1R(DE3)
    Expression System Taxid: 469008
    Organism Scientific: AMYCOLATOPSIS SP. ATCC 39116
    Organism Taxid: 385957

 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  (3, 42)

Asymmetric Unit (3, 42)
No.NameCountTypeFull Name
1ACT38Ligand/IonACETATE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 26)
No.NameCountTypeFull Name
1ACT25Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1ACT13Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:186 , TYR A:190 , VAL A:191 , ASP A:192 , GLY A:193 , ARG A:194 , SER A:195 , GLN A:251 , HIS A:323 , ILE A:324 , THR A:327 , ASN A:328 , ARG A:330 , ARG A:348 , PHE A:378 , PHE A:389 , GLN A:393 , ILE A:417 , VAL A:447 , HOH A:611 , HOH A:628 , HOH A:629 , HOH A:710BINDING SITE FOR RESIDUE HEM A 501
02AC2SOFTWAREGLU A:260 , GLU A:286 , HOH A:677BINDING SITE FOR RESIDUE MN A 502
03AC3SOFTWAREGLU A:224 , LYS A:343 , SER A:383 , ASN A:387 , GLN A:388BINDING SITE FOR RESIDUE ACT A 503
04AC4SOFTWAREPRO A:302 , GLY A:304 , HOH A:633 , GLN B:294BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREARG A:208 , VAL A:214 , ASP A:218BINDING SITE FOR RESIDUE ACT A 505
06AC6SOFTWAREASP A:216 , SER A:308 , ASP A:310 , ARG A:367BINDING SITE FOR RESIDUE ACT A 506
07AC7SOFTWAREGLY A:315 , PRO A:319 , PHE A:320 , LYS A:426 , TYR A:427 , ACT A:508 , HOH A:711BINDING SITE FOR RESIDUE ACT A 507
08AC8SOFTWARESER A:409 , PRO A:411 , ACT A:507 , HOH A:746BINDING SITE FOR RESIDUE ACT A 508
09AC9SOFTWARESER A:311 , ASP A:312 , LYS A:313 , LEU A:314 , HOH A:795 , ASP B:209 , ACT B:511BINDING SITE FOR RESIDUE ACT A 509
10BC1SOFTWAREALA A:34 , ARG A:37BINDING SITE FOR RESIDUE ACT A 510
11BC2SOFTWARELYS A:120 , GLY A:386 , GLU A:390 , PHE A:391 , GLN A:394 , HOH A:708BINDING SITE FOR RESIDUE ACT A 511
12BC3SOFTWAREASP A:205 , ARG A:208 , ASP A:209BINDING SITE FOR RESIDUE ACT A 512
13BC4SOFTWAREASP A:192 , GLY A:350 , HOH A:831BINDING SITE FOR RESIDUE ACT A 513
14BC5SOFTWAREASN A:58 , LEU A:466BINDING SITE FOR RESIDUE ACT A 514
15BC6SOFTWAREARG A:254 , GLU A:340 , LYS A:343BINDING SITE FOR RESIDUE ACT A 515
16BC7SOFTWAREALA A:112 , PRO A:406 , ASP A:407 , GLY A:408BINDING SITE FOR RESIDUE ACT A 516
17BC8SOFTWAREGLU A:73 , VAL A:74 , VAL A:83 , GLY A:84 , HOH A:707BINDING SITE FOR RESIDUE ACT A 517
18BC9SOFTWAREARG A:39 , LEU A:40 , THR A:41 , GLY A:174BINDING SITE FOR RESIDUE ACT A 518
19CC1SOFTWAREALA A:98 , THR A:99 , ALA A:335 , ILE A:395 , ASN A:399BINDING SITE FOR RESIDUE ACT A 519
20CC2SOFTWARETHR A:9 , SER A:220 , ALA A:221 , PRO A:222 , ACT A:527 , HOH A:754BINDING SITE FOR RESIDUE ACT A 520
21CC3SOFTWAREPRO A:197 , PRO A:219 , SER A:220 , ALA A:221 , GLN A:225 , ARG A:342 , LEU A:345 , HOH A:809BINDING SITE FOR RESIDUE ACT A 521
22CC4SOFTWAREALA A:34 , PRO A:197 , LEU A:198 , ARG A:349 , HOH A:768BINDING SITE FOR RESIDUE ACT A 522
23CC5SOFTWARELEU A:413 , ARG A:422 , ALA A:423 , GLN A:425 , PRO A:442 , ILE A:443BINDING SITE FOR RESIDUE ACT A 523
24CC6SOFTWAREPRO A:108 , THR A:111 , ALA A:112 , ASP A:407BINDING SITE FOR RESIDUE ACT A 524
25CC7SOFTWARESER A:109 , ALA A:112 , GLY A:113 , ALA A:116 , ALA A:117 , LYS A:120 , GLU A:390BINDING SITE FOR RESIDUE ACT A 525
26CC8SOFTWAREGLY A:176 , LEU A:177 , ALA A:178BINDING SITE FOR RESIDUE ACT A 526
27CC9SOFTWARETHR A:10 , THR A:201 , VAL A:204 , SER A:220 , HIS A:357 , ACT A:520BINDING SITE FOR RESIDUE ACT A 527
28DC1SOFTWAREGLU B:186 , TYR B:190 , VAL B:191 , ASP B:192 , GLY B:193 , ARG B:194 , SER B:195 , GLN B:251 , ARG B:284 , HIS B:323 , THR B:327 , ASN B:328 , ARG B:330 , ARG B:348 , PHE B:378 , PHE B:389 , ILE B:417 , HOH B:618 , HOH B:619BINDING SITE FOR RESIDUE HEM B 501
29DC2SOFTWAREGLU B:260 , GLU B:286 , ACT B:514BINDING SITE FOR RESIDUE MN B 502
30DC3SOFTWAREARG A:208 , ASP A:209 , SER B:311 , ASP B:312 , LYS B:313 , LEU B:314BINDING SITE FOR RESIDUE ACT B 503
31DC4SOFTWAREASN A:215 , PRO A:365 , ARG A:367 , ASP B:310 , HOH B:734BINDING SITE FOR RESIDUE ACT B 504
32DC5SOFTWAREPRO B:415 , ARG B:422 , ALA B:423 , GLN B:425 , PRO B:442 , ILE B:443 , HOH B:607BINDING SITE FOR RESIDUE ACT B 505
33DC6SOFTWAREGLY B:315 , PRO B:319 , PHE B:320 , HIS B:321 , LYS B:426 , TYR B:427BINDING SITE FOR RESIDUE ACT B 506
34DC7SOFTWAREVAL B:36 , HIS B:70 , GLU B:73 , VAL B:74 , VAL B:83 , HOH B:733BINDING SITE FOR RESIDUE ACT B 507
35DC8SOFTWAREARG B:39 , LEU B:40 , THR B:41 , GLY B:174BINDING SITE FOR RESIDUE ACT B 508
36DC9SOFTWAREALA B:106 , VAL B:228 , PRO B:229 , TYR B:243 , HOH B:753BINDING SITE FOR RESIDUE ACT B 509
37EC1SOFTWAREASP A:310 , SER A:311 , ARG B:208 , ASN B:215BINDING SITE FOR RESIDUE ACT B 510
38EC2SOFTWAREACT A:509 , ARG B:208 , ASP B:209BINDING SITE FOR RESIDUE ACT B 511
39EC3SOFTWARELYS B:33 , ALA B:34 , ARG B:349 , HOH B:666BINDING SITE FOR RESIDUE ACT B 512
40EC4SOFTWARETHR B:93 , ALA B:94 , HIS B:95 , ILE B:137 , GLU B:453 , HOH B:645 , HOH B:732BINDING SITE FOR RESIDUE ACT B 513
41EC5SOFTWARETYR B:190 , GLU B:275 , PHE B:285 , GLU B:286 , MN B:502 , HOH B:655BINDING SITE FOR RESIDUE ACT B 514
42EC6SOFTWAREASP A:209 , HOH A:706 , GLN B:316 , GLY B:432BINDING SITE FOR RESIDUE ACT B 515

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G2C)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1His A:301 -Pro A:302
2Phe A:402 -Pro A:403
3Asp B:287 -Gly B:288
4His B:301 -Pro B:302
5Phe B:402 -Pro B:403

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4G2C)

(-) 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:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhh...........eeeeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeeee.ee.....ee..............hhhhhhhhhhhh..........hhhhh.ee..........eeeeeeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......................................hhhhhhh........hhhhhhhhh.ee..eee...........hhhhh.....eeeeeeee.....hhhhhhhh..............................ee.........ee........eeeeeeeeeee.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g2c A   5 VDLSTTLSWKSATGEAATMLDELQPNILKAHVRDRLTVLFLGFGDAAEARTFLNGLSGLMKSARTHLQEVEAHKLTKAVGTPYLGVGLTAHGYATLGVTAPADPSFTAGAKAAVEKLADPAVTEWEGHYQQTIDAVLLLGDATAGPVRTLRRQVEALRPASVTVVGEESGLGLANANGDGIEHFGYVDGRSQPLFLTEDVDAERDTTDGVNDWDPSAPLEQVLVPDPAAPDPTVHFGSYFVFRKLEQNVRLFKEAERDLAHDLGLRGEDRERAGAMLVGRFEDGTPLTAQSAPGSHHPVGNDFSYDSDKLGQKCPFHAHIRKTNPRGSGGAEAPEEERKHLMARRGQTYGRRHDDPNADLPPRLRPAKDVGLLFMAFNSNLGNQFEFTQQIWANNPAFPFPPDGSQPGLDPVIGQGARAPQKYAPEWGHNNVAEATDPIPQAVTMKGGEYFFMPSLAFLRSL 466
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464  


Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh...........eeeeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhh.....eeeeeeeeee.ee.....ee..............hhhhhhhhhhhh..........hhhhh.ee..........eeeeeeeeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......................................hhhhhhh........hhhhhhhhh.ee..eee...........hhhhh.....eeeeeeee.....hhhhhhhhh.............................ee.........ee........eeeeeeeeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g2c B   4 PVDLSTTLSWKSATGEAATMLDELQPNILKAHVRDRLTVLFLGFGDAAEARTFLNGLSGLMKSARTHLQEVEAHKLTKAVGTPYLGVGLTAHGYATLGVTAPADPSFTAGAKAAVEKLADPAVTEWEGHYQQTIDAVLLLGDATAGPVRTLRRQVEALRPASVTVVGEESGLGLANANGDGIEHFGYVDGRSQPLFLTEDVDAERDTTDGVNDWDPSAPLEQVLVPDPAAPDPTVHFGSYFVFRKLEQNVRLFKEAERDLAHDLGLRGEDRERAGAMLVGRFEDGTPLTAQSAPGSHHPVGNDFSYDSDKLGQKCPFHAHIRKTNPRGSGGAEAPEEERKHLMARRGQTYGRRHDDPNADLPPRLRPAKDVGLLFMAFNSNLGNQFEFTQQIWANNPAFPFPPDGSQPGLDPVIGQGARAPQKYAPEWGHNNVAEATDPIPQAVTMKGGEYFFMPSLAFLRSL 466
                                    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       453       463
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 4G2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G2C)

(-) Gene Ontology  (10, 10)

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