1LGA - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC REFINEMENT OF LIGNIN PEROXIDASE AT 2 ANGSTROMS

Authors :   T. L. Poulos, S. L. Edwards, H. Wariishi, M. H. Gold

Date :   08 Dec 92 (Deposition) - 31 Oct 93 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. L. Poulos, S. L. Edwards, H. Wariishi, M. H. Gold
Crystallographic Refinement Of Lignin Peroxidase At 2 A.
J. Biol. Chem. V. 268 4429 1993
PubMed-ID: 8440725
(for further references see the PDB file header)

Molecule 1 - LIGNIN PEROXIDASE
	Chains	:	A, B
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Organism Scientific	:	PHANEROCHAETE CHRYSOSPORIUM
	Organism Taxid	:	5306

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:257 , LYS A:260	BINDING SITE FOR RESIDUE NAG A 397
02	AC2	SOFTWARE	ASN B:257 , LYS B:260 , HOH B:617	BINDING SITE FOR RESIDUE NAG B 397
03	AC3	SOFTWARE	SER A:177 , ASP A:194 , THR A:196 , ILE A:199 , ASP A:201	BINDING SITE FOR RESIDUE CA A 398
04	AC4	SOFTWARE	ASP A:48 , GLY A:66 , ASP A:68 , SER A:70 , HOH A:473 , HOH A:511	BINDING SITE FOR RESIDUE CA A 399
05	AC5	SOFTWARE	SER B:177 , ASP B:194 , THR B:196 , ILE B:199 , ASP B:201	BINDING SITE FOR RESIDUE CA B 398
06	AC6	SOFTWARE	ASP B:48 , GLY B:66 , ASP B:68 , SER B:70 , HOH B:459 , HOH B:499	BINDING SITE FOR RESIDUE CA B 399
07	AC7	SOFTWARE	HIS A:39 , GLU A:40 , ARG A:43 , PHE A:46 , ILE A:85 , GLU A:146 , ILE A:154 , MET A:172 , LEU A:173 , ALA A:175 , HIS A:176 , VAL A:178 , ALA A:179 , ALA A:180 , VAL A:181 , ASN A:182 , ASP A:183 , PHE A:193 , ILE A:235 , THR A:237 , HOH A:433 , HOH A:446 , HOH A:471 , HOH A:519	BINDING SITE FOR RESIDUE HEM A 396
08	AC8	SOFTWARE	HIS B:39 , GLU B:40 , ILE B:42 , ARG B:43 , PHE B:46 , ILE B:85 , GLU B:146 , PRO B:147 , ILE B:154 , 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 , THR B:237 , HOH B:435 , HOH B:458 , HOH B:506 , HOH B:507	BINDING SITE FOR RESIDUE HEM B 396
09	HPA	AUTHOR	ASP A:238	RESIDUE IN CHAIN A THAT H-BONDS WITH PROXIMAL HIS 176
10	HPB	AUTHOR	ASP B:238	RESIDUE IN CHAIN B THAT H-BONDS WITH PROXIMAL HIS 176
11	PBA	AUTHOR	ARG A:43 , PHE A:46 , HIS A:47	DISTAL RESIDUES IN CHAIN A FORMING THE PEROXIDE BINDING POCKET. THIS IS ANALOGOUS TO THE ARG-TRP-HIS FOUND IN CYTOCHROME C PEROXIDASE
12	PBB	AUTHOR	ARG B:43 , PHE B:46 , HIS B:47	DISTAL RESIDUES IN CHAIN B FORMING THE PEROXIDE BINDING POCKET. THIS IS ANALOGOUS TO THE ARG-TRP-HIS FOUND IN CYTOCHROME C PEROXIDASE
13	PHA	AUTHOR	HIS A:176	RESIDUES BOUND TO PROXIMAL HEME LIGAND, CHAIN A
14	PHB	AUTHOR	HIS B:176	RESIDUES BOUND TO PROXIMAL HEME LIGAND, CHAIN B

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 1LGA)

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_2	PS00436	Peroxidases active site signature.	LIG2_PHACH	66-77	2	A:38-49 B:38-49
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG2_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.	LIG2_PHACH	66-77	1	A:38-49 -
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG2_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.	LIG2_PHACH	66-77	1	- B:38-49
2	PEROXIDASE_1	PS00435	Peroxidases proximal heme-ligand signature.	LIG2_PHACH	196-206	1	- B:168-178

(no "Exon" information available for 1LGA)

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:343
 aligned with LIG2_PHACH | P49012 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:343
                                    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   
           LIG2_PHACH    29 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPHKA 371
               SCOP domains d1lgaa_ A: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------1lgaA01 A:11-144,A:269-299  [code=1.10.520.10, no name defined]                                                                       1lgaA02 A:145-268,A:300-339 Peroxidase, domain 2                                                                            1lgaA01 A:11-144,A:269-299     1lgaA02 A:145-268,A:300-339             ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhh............hhhhhhhhh........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhh................ee........eehhhhhh......hhhhhh....hhhhhhhhhhhhhhhh.........ee........................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lga A   1 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPHKA 343
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with LIG2_PHACH | P49012 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:341
                                    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 
           LIG2_PHACH    29 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPH 369
               SCOP domains d1lgab_ B: Fungal peroxidase (ligninase)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------1lgaB01 B:11-144,B:269-296  [code=1.10.520.10, no name defined]                                                                       1lgaB02 B:145-268,B:297-339 Peroxidase, domain 2                                                                            1lgaB01 B:11-144,B:269-296  1lgaB02 B:145-268,B:297-339                -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh........hhhhhhhhhhhhhh....hhhh............hhhhhhhhh........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........ee....................hhhhhhhhhhhh...hhhhhhhhhhhh..ee.........ee..........hhhhh................ee........eehhhhhh......hhhhhh....hhhhhhhhhhhhhhhh.........ee......................................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2----------------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lga B   1 ATCANGKTVGDASCCAWFDVLDDIQANMFHGGQCGAEAHESIRLVFHDSIAISPAMEAKGKFGGGGADGSIMIFDTIETAFHPNIGLDEVVAMQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRKPATQPAPDGLVPEPFHTVDQIIARVNDAGEFDELELVWMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQFRGTLFPGSGGNQGEVESGMAGEIRIQTDHTLARDSRTACEWQSFVGNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPLSKPIPGNGPFSFFPPGKSHSDIEQACAETPFPSLVTLPGPATSVARIPPH 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

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( (-)

)

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	d1lgaa_	A:
1b	d1lgab_	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)

Phanerochaete chrysosporium. Organism_taxid: 5306 (5)

1a	1lgaA01	A:11-144,A:269-299
1b	1lgaB01	B:11-144,B:269-296

Topology: Peroxidase; domain 2 (241)

Homologous Superfamily: Peroxidase, domain 2 (241)

Phanerochaete chrysosporium. Organism_taxid: 5306 (5)

2a	1lgaA02	A:145-268,A:300-339
2b	1lgaB02	B:145-268,B:297-339

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (LIG2_PHACH | P49012)

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: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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(no "Related Entries Specified in the PDB File" available for 1LGA)

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Ligands, Modified Residues, Ions (3, 8)

Sites (14, 14)

SS Bonds (8, 8)

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