1B85 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   LIGNIN PEROXIDASE

Authors :   W. Blodig, W. A. Doyle, A. T. Smith, K. Piontek

Date :   05 Feb 99 (Deposition) - 16 Feb 99 (Release) - 23 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Lignin Degradation, Heme, Radical Reaction, Electron Transfer, Oxidoreductase, Calcium, Cleavage On Pair Of Basic Residues, Disulfide Bond, Glycoprotein, Hydrogen Peroxide, Iron, Metal-Binding, Peroxidase, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Blodig, A. T. Smith, W. A. Doyle, K. Piontek
Crystal Structures Of Pristine And Oxidatively Processed Lignin Peroxidase Expressed In Escherichia Coli And Of The W171F Variant That Eliminates The Redox Active Tryptophan 171. Implications For The Reaction Mechanism.
J. Mol. Biol. V. 305 851 2001
PubMed-ID: 11162097 | Reference-DOI: 10.1006/JMBI.2000.4346
(for further references see the PDB file header)

Molecule 1 - LIGNINASE H8
	Chains	:	A, B
	EC Number	:	1.11.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFLAG1-LIPP
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector	:	PFLAG1
	Expression System Vector Type	:	PLASMID
	Fragment	:	MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
	Gene	:	LIP H8, LPOA
	Mutation	:	YES
	Organism Common	:	WHITE-ROT FUNGUS
	Organism Scientific	:	PHANEROCHAETE CHRYSOSPORIUM
	Organism Taxid	:	5306
	Other Details	:	HEME CONTAINING
	Strain	:	BKM 1767
	Synonym	:	DIARYLPROPANE PEROXIDASE, LIGNIN PEROXIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:48 , GLY A:66 , ASP A:68 , SER A:70 , HOH A:458 , HOH A:565	BINDING SITE FOR RESIDUE CA A 1351
2	AC2	SOFTWARE	SER A:177 , ASP A:194 , THR A:196 , ILE A:199 , ASP A:201	BINDING SITE FOR RESIDUE CA A 1352
3	AC3	SOFTWARE	ASP B:48 , GLY B:66 , ASP B:68 , SER B:70 , HOH B:576 , HOH B:577	BINDING SITE FOR RESIDUE CA B 2351
4	AC4	SOFTWARE	SER B:177 , ASP B:194 , THR B:196 , ILE B:199 , ASP B:201	BINDING SITE FOR RESIDUE CA B 2352
5	AC5	SOFTWARE	HIS A:39 , GLU A:40 , ILE A:42 , ARG A:43 , PHE A:46 , ILE A:85 , GLU A:146 , MET A:172 , LEU A:173 , ALA A:175 , HIS A:176 , ALA A:179 , ALA A:180 , VAL A:181 , ASN A:182 , ASP A:183 , PHE A:193 , ILE A:235 , SER A:237 , HOH A:362 , HOH A:413 , HOH A:446 , HOH A:460 , HOH A:491	BINDING SITE FOR RESIDUE HEM A 350
6	AC6	SOFTWARE	HIS B:39 , GLU B:40 , ILE B:42 , ARG B:43 , PHE B:46 , ILE B:85 , GLU B:146 , MET B:172 , LEU B:173 , ALA B:175 , HIS B:176 , ALA B:179 , ALA B:180 , VAL B:181 , ASN B:182 , ASP B:183 , PHE B:193 , ILE B:235 , SER B:237 , HOH B:361 , HOH B:420 , HOH B:467 , HOH B:527 , HOH B:541	BINDING SITE FOR RESIDUE HEM B 350

Asymmetric Unit

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

(no "Cis Peptide Bond" information available for 1B85)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LIG8_PHACH_002 *	R	142	A	LIG8_PHACH	---	---	A/B	A	114	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LIG8_PHACH_002 *	R	142	A	LIG8_PHACH	---	---	A	A	114	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LIG8_PHACH_002 *	R	142	A	LIG8_PHACH	---	---	B	A	114	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	LIG8_PHACH	66-77	2	A:38-49 B:38-49
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG8_PHACH	196-206	2	A:168-178 B:168-178

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	LIG8_PHACH	66-77	1	A:38-49 -
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG8_PHACH	196-206	1	A:168-178 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	LIG8_PHACH	66-77	1	- B:38-49
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG8_PHACH	196-206	1	- B:168-178

(no "Exon" information available for 1B85)

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:348
 aligned with LIG8_PHACH | P06181 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:348
                                    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        
           LIG8_PHACH    25 IEKRATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGRVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA 372
               SCOP domains d1b85a_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------1b85A01 A:11-144,A:269-296  [code=1.10.520.10, no name defined]                                                                       1b85A02 A:145-268,A:297-339 Peroxidase, domain 2                                                                            1b85A01 A:11-144,A:269-296  1b85A02 A:145-268,A:297-339                ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.....ee..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhhh..........hhhh.hhhhhh.hhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhhhh..............ee........eehhhhhh......hhhhhhh...hhhhhhhhhhhhhhhhh....hhh.ee.hhh.....................hhh................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b85 A  -3 IEKRATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVFMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA 344
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain B from PDB  Type:PROTEIN  Length:345
 aligned with LIG8_PHACH | P06181 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:345
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367     
           LIG8_PHACH    28 RATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGRVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA 372
               SCOP domains d1b85b_ B: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -----------1b85B01 B:11-144,B:269-296  [code=1.10.520.10, no name defined]                                                                       1b85B02 B:145-268,B:297-339 Peroxidase, domain 2                                                                            1b85B01 B:11-144,B:269-296  1b85B02 B:145-268,B:297-339                ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....ee..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhhhh..........hhhh.hhhhhh.hhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhhhh..............ee........eehhhhhh......hhhhhhh...hhhhhhhhhhhhhhhhh....hhh.ee.hhh.....................hhh................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b85 B   0 RATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVFMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA 344
                                     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       299       309       319       329       339

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Heme-dependent peroxidases (402)

Superfamily: Heme-dependent peroxidases (402)

Family: CCP-like (292)

Protein domain: Fungal peroxidase (ligninase) (28)

Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306] (9)

1a	d1b85a_	A:
1b	d1b85b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Peroxidase; domain 1 (244)

Homologous Superfamily: [code=1.10.520.10, no name defined] (241)

White-rot fungus (Phanerochaete chrysosporium) (1)

1a	1b85A01	A:11-144,A:269-296
1b	1b85B01	B:11-144,B:269-296

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

White-rot fungus (Phanerochaete chrysosporium) (1)

2a	1b85A02	A:145-268,A:297-339
2b	1b85B02	B:145-268,B:297-339

(no "Pfam Domain" information available for 1B85)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LIG8_PHACH | P06181)

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.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 1b85)

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	1b85
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(no "Related Entries Specified in the PDB File" available for 1B85)

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