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(-) Description

Title :  LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)
 
Authors :  T. H. Choinowski, K. Piontek
Date :  08 Oct 96  (Deposition) - 11 Jan 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Lignin Degradation, Heme, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Choinowski, W. Blodig, K. H. Winterhalter, K. Piontek
The Crystal Structure Of Lignin Peroxidase At 1. 70 A Resolution Reveals A Hydroxy Group On The Cbeta Of Tryptophan 171: A Novel Radical Site Formed During The Redo Cycle.
J. Mol. Biol. V. 286 809 1999
PubMed-ID: 10024453  |  Reference-DOI: 10.1006/JMBI.1998.2507
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGNIN PEROXIDASE
    Atcc: 24725
    Chains: A, B
    EC Number: 1.11.1.-
    Organism Scientific: PHANEROCHAETE CHRYSOSPORIUM
    Organism Taxid: 5306
    Other Details: ISOZYME LIP4.65
    Strain: BKM-F1267

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4HTR2Mod. Amino AcidBETA-HYDROXYTRYPTOPHANE
5MAN7Ligand/IonALPHA-D-MANNOSE
6NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:257 , LYS A:260 , HOH A:852 , GLY B:5BINDING SITE FOR RESIDUE NAG A 360
02AC2SOFTWARESER A:334 , VAL A:335 , HOH A:473 , HOH A:475BINDING SITE FOR RESIDUE MAN A 370
03AC3SOFTWAREPRO A:228 , LEU A:229 , LYS A:230 , LYS A:308 , SER A:332 , ALA A:333 , HOH A:469BINDING SITE FOR RESIDUE MAN A 375
04AC4SOFTWAREASN B:257 , LYS B:260 , NAG B:361 , FUC B:365BINDING SITE FOR RESIDUE NAG B 360
05AC5SOFTWARENAG B:360BINDING SITE FOR RESIDUE NAG B 361
06AC6SOFTWAREGLU B:250 , SER B:253 , LYS B:260 , NAG B:360 , MAN B:380 , HOH B:582 , HOH B:591BINDING SITE FOR RESIDUE FUC B 365
07AC7SOFTWAREHOH A:440 , SER B:334 , VAL B:335 , ALA B:336 , HOH B:524 , HOH B:526BINDING SITE FOR RESIDUE MAN B 370
08AC8SOFTWAREPRO B:228 , LEU B:229 , LYS B:230 , LYS B:308 , SER B:332 , ALA B:333 , HOH B:520BINDING SITE FOR RESIDUE MAN B 375
09AC9SOFTWARECYS B:317 , SER B:319 , THR B:320 , FUC B:365 , HOH B:589 , HOH B:592BINDING SITE FOR RESIDUE MAN B 380
10BC1SOFTWAREHIS B:310 , THR B:324 , MAN B:386BINDING SITE FOR RESIDUE MAN B 385
11BC2SOFTWAREASN B:11 , ILE B:283 , HIS B:310 , ALA B:311 , MAN B:385BINDING SITE FOR RESIDUE MAN B 386
12BC3SOFTWARESER A:177 , ASP A:194 , THR A:196 , GLN A:199 , ASP A:201BINDING SITE FOR RESIDUE CA A 351
13BC4SOFTWAREASP A:48 , GLY A:66 , ASP A:68 , SER A:70 , HOH A:709 , HOH A:710BINDING SITE FOR RESIDUE CA A 352
14BC5SOFTWARESER B:177 , ASP B:194 , THR B:196 , GLN B:199 , ASP B:201BINDING SITE FOR RESIDUE CA B 351
15BC6SOFTWAREASP B:48 , GLY B:66 , ASP B:68 , SER B:70 , HOH B:404 , HOH B:405BINDING SITE FOR RESIDUE CA B 352
16BC7SOFTWAREHIS A:39 , GLU A:40 , ARG A:43 , PHE A:46 , ILE A:85 , GLU A:146 , PRO A:147 , LEU A:172 , LEU A:173 , ALA A:175 , HIS A:176 , ALA A:179 , ALA A:180 , ALA A:181 , ASN A:182 , ASP A:183 , VAL A:184 , LEU A:235 , THR A:237 , HOH A:398 , HOH A:755 , HOH A:757 , HOH A:758 , HOH A:779BINDING SITE FOR RESIDUE HEM A 350
17BC8SOFTWAREHIS B:39 , GLU B:40 , ARG B:43 , PHE B:46 , ILE B:85 , GLU B:146 , PRO B:147 , LEU B:172 , LEU B:173 , ALA B:175 , HIS B:176 , ALA B:179 , ALA B:180 , ALA B:181 , ASN B:182 , ASP B:183 , VAL B:184 , LEU B:235 , THR B:237 , HOH B:399 , HOH B:419 , HOH B:421 , HOH B:423BINDING SITE FOR RESIDUE HEM B 350
18HE3UNKNOWNHEM A:350 , HEM B:350HEM 350

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:15
2A:14 -A:285
3A:34 -A:120
4A:249 -A:317
5B:2 -B:15
6B:14 -B:285
7B:34 -B:120
8B:249 -B:317

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_2PS00436 Peroxidases active site signature.LIG4_PHACH67-78
 		  2A:38-49
B:38-49
2PEROXIDASE_1PS00435 Peroxidases proximal heme-ligand signature.LIG4_PHACH197-207
 		  2A:168-178
B:168-178

(-) Exons   (0, 0)

(no "Exon" information available for 1QPA)

(-) 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:344
 aligned with LIG4_PHACH | P11542 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:344
                                    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       368    
           LIG4_PHACH    29 VACPDGVHTASNAACCAWFPVLDDIQQNLFHGGQCGAEAHEALRMVFHDSIAISPKLQSQGKFGGGGADGSIITFSSIETTYHPNIGLDEVVAIQKPFIAKHGVTRGDFIAFAGAVGVSNCPGAPQMQFFLGRPEATQAAPDGLVPEPFHTIDQVLARMLDAGGFDEIETVWLLSAHSIAAANDVDPTISGLPFDSTPGQFDSQFFVETQLRGTAFPGKTGIQGTVMSPLKGEMRLQTDHLFARDSRTACEWQSFVNNQTKLQEDFQFIFTALSTLGHDMNAMTDCSEVIPAPKPVNFGPSFFPAGKTHADIEQACASTPFPTLITAPGPSASVARIPPPPSPN 372
               SCOP domains d1qpaa_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----------1qpaA01 A:11-144,A:269-296  [code=1.10.520.10, no name defined]                                                                       1qpaA02 A:145-268,A:298-339 Peroxidase, domain 2                                                                            1qpaA01 A:11-144,A:269-296  1qpaA02 A:145-268,A:298-339              ------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhh...........hhhh.hhhh...hhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhh................ee........eehhhhhhhh..............hhhhhhhhhhhhhhhh.....hhh.ee.hhh............ee.....hhh.............ee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qpa A   0 VACPDGVHTASNAACCAWFPVLDDIQQNLFHGGQCGAEAHEALRMVFHDSIAISPKLQSQGKFGGGGADGSIITFSSIETTYHPNIGLDEVVAIQKPFIAKHGVTPGDFIAFAGAVGVSNCPGAPQMQFFLGRPEATQAAPDGLVPEPFHTIDQVLARMLDAGGFDEIETVwLLSAHSIAAANDVDPTISGLPFDSTPGQFDSQFFVETQLRGTAFPGKTGIQGTVMSPLKGEMRLQTDHLFARDSRTACEWQSFVNNQTKLQEDFQFIFTALSTLGHDMNAMIDCSEVIPAPKPVNFGPSFFPAGKTHADIEQACASTPFPTLITAPGPSASVARIPPPPSPN 345
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 |     179       189       199       209       219       229       239       249       259       269       279       289      |300|      311       321       331       341    
                                                                                                                                                                                                     171-HTR                                                                                                                      296| ||                                           
                                                                                                                                                                                                                                                                                                                                   298 ||                                           
                                                                                                                                                                                                                                                                                                                                     300|                                           
                                                                                                                                                                                                                                                                                                                                      302                                           


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with LIG4_PHACH | P11542 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:344
                                    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       368    
           LIG4_PHACH    29 VACPDGVHTASNAACCAWFPVLDDIQQNLFHGGQCGAEAHEALRMVFHDSIAISPKLQSQGKFGGGGADGSIITFSSIETTYHPNIGLDEVVAIQKPFIAKHGVTRGDFIAFAGAVGVSNCPGAPQMQFFLGRPEATQAAPDGLVPEPFHTIDQVLARMLDAGGFDEIETVWLLSAHSIAAANDVDPTISGLPFDSTPGQFDSQFFVETQLRGTAFPGKTGIQGTVMSPLKGEMRLQTDHLFARDSRTACEWQSFVNNQTKLQEDFQFIFTALSTLGHDMNAMTDCSEVIPAPKPVNFGPSFFPAGKTHADIEQACASTPFPTLITAPGPSASVARIPPPPSPN 372
               SCOP domains d1qpab_ B: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----------1qpaB01 B:11-144,B:269-296  [code=1.10.520.10, no name defined]                                                                       1qpaB02 B:145-268,B:298-339 Peroxidase, domain 2                                                                            1qpaB01 B:11-144,B:269-296  1qpaB02 B:145-268,B:298-339              ------ CATH domains
           Pfam domains (1) --------------------peroxidase-1qpaB03 B:20-257                                                                                                                                                                                                                   -DUF3415-1qpaB01 B:259-341                                                        ---- Pfam domains (1)
           Pfam domains (2) --------------------peroxidase-1qpaB04 B:20-257                                                                                                                                                                                                                   -DUF3415-1qpaB02 B:259-341                                                        ---- Pfam domains (2)
         Sec.struct. author ............hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhh............hhhh.hhhh...hhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhh................ee........eehhhhhhhh..............hhhhhhhhhhhhhhhh.....hhh.ee.hhh............ee.....hhh.............ee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qpa B   0 VACPDGVHTASNAACCAWFPVLDDIQQNLFHGGQCGAEAHEALRMVFHDSIAISPKLQSQGKFGGGGADGSIITFSSIETTYHPNIGLDEVVAIQKPFIAKHGVTPGDFIAFAGAVGVSNCPGAPQMQFFLGRPEATQAAPDGLVPEPFHTIDQVLARMLDAGGFDEIETVwLLSAHSIAAANDVDPTISGLPFDSTPGQFDSQFFVETQLRGTAFPGKTGIQGTVMSPLKGEMRLQTDHLFARDSRTACEWQSFVNNQTKLQEDFQFIFTALSTLGHDMNAMIDCSEVIPAPKPVNFGPSFFPAGKTHADIEQACASTPFPTLITAPGPSASVARIPPPPSPN 345
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 |     179       189       199       209       219       229       239       249       259       269       279       289      |300|      311       321       331       341    
                                                                                                                                                                                                     171-HTR                                                                                                                      296| ||                                           
                                                                                                                                                                                                                                                                                                                                   298 ||                                           
                                                                                                                                                                                                                                                                                                                                     300|                                           
                                                                                                                                                                                                                                                                                                                                      302
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3415] (12)
(-)
Clan: no clan defined [family: peroxidase] (92)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LIG4_PHACH | P11542)
molecular function
    GO:0016690    diarylpropane peroxidase activity    Catalysis of the reaction: (3,4-dimethoxyphenyl)methanol + H2O2 = 3,4-dimethoxybenzaldehyde + 2 H2O.
    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:0046274    lignin catabolic process    The chemical reactions and pathways resulting in the breakdown of lignins, a class of polymers of phenylpropanoid units.
    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.

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