3FM1 - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII

Authors :   K. Piontek, A. T. Martinez, T. Choinowski, D. A. Plattner

Date :   19 Dec 08 (Deposition) - 22 Dec 09 (Release) - 22 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym./Biol. Unit : A

Keywords :   Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Electron Transfer, Lignin Peroxidase, Lignin Degradation, Manganese Peroxidase, Mn-Independent Oxidation Phenolic Non-Phenolic Aromatics, Mnii Oxidation, Peroxidase, Polyvalent Peroxidase, Oxidoreductase, Calcium, Heme, Hydrogen Peroxide, Iron, Manganese, Metal-Binding, Organic Radical, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Piontek, T. Choinowski, M. Perez-Boada, F. J. Ruiz-Duenas, M. J. Martinez, D. A. Plattner, A. T. Martinez
Structural And Site-Directed Mutagenesis Study Of Versatile Peroxidase Oxidizing Both Mn(Ii) And Aromatic Substrates
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:36 , HIS A:39 , GLU A:40 , LEU A:42 , ARG A:43 , PHE A:46 , GLU A:140 , PRO A:141 , LEU A:165 , LEU A:166 , SER A:168 , HIS A:169 , ALA A:172 , ALA A:173 , ALA A:174 , ASP A:175 , LYS A:176 , VAL A:177 , PHE A:186 , LEU A:228 , SER A:230 , MN A:353 , HOH A:434 , HOH A:470 , HOH A:805 , HOH A:1159 , HOH A:1160	BINDING SITE FOR RESIDUE HEM A 350
02	AC2	SOFTWARE	ASP A:48 , GLY A:60 , ASP A:62 , SER A:64 , HOH A:346 , HOH A:816	BINDING SITE FOR RESIDUE CA A 351
03	AC3	SOFTWARE	SER A:170 , ASP A:187 , THR A:189 , VAL A:192 , ASP A:194	BINDING SITE FOR RESIDUE CA A 352
04	AC4	SOFTWARE	GLU A:36 , GLU A:40 , ASP A:175 , HEM A:350 , HOH A:1158 , HOH A:1159	BINDING SITE FOR RESIDUE MN A 353
05	AC5	SOFTWARE	ASP A:30 , GLU A:37 , HIS A:232 , HOH A:420	BINDING SITE FOR RESIDUE ZN A 332
06	AC6	SOFTWARE	GLU A:26 , ASP A:237 , NA A:338 , HOH A:530 , HOH A:532 , HOH A:534 , HOH A:1174	BINDING SITE FOR RESIDUE ZN A 333
07	AC7	SOFTWARE	HIS A:293 , ASP A:318 , HOH A:1053 , HOH A:1129 , HOH A:1130 , HOH A:1133	BINDING SITE FOR RESIDUE FE A 334
08	AC8	SOFTWARE	GLU A:36 , GLU A:40 , GLU A:83 , FE A:336 , HOH A:432 , HOH A:755 , HOH A:1166 , HOH A:1167	BINDING SITE FOR RESIDUE ZN A 335
09	AC9	SOFTWARE	GLU A:83 , ASP A:175 , ZN A:335 , HOH A:1163 , HOH A:1164 , HOH A:1165 , HOH A:1166 , HOH A:1167	BINDING SITE FOR RESIDUE FE A 336
10	BC1	SOFTWARE	NA A:340 , HOH A:508 , HOH A:512 , HOH A:513 , HOH A:1171 , HOH A:1175	BINDING SITE FOR RESIDUE FE A 337
11	BC2	SOFTWARE	ASP A:146 , ZN A:333 , HOH A:528 , HOH A:529 , HOH A:530 , HOH A:532 , HOH A:864 , HOH A:1174	BINDING SITE FOR RESIDUE NA A 338
12	BC3	SOFTWARE	HOH A:940 , HOH A:941 , HOH A:942 , HOH A:943 , HOH A:944 , HOH A:945	BINDING SITE FOR RESIDUE NA A 339
13	BC4	SOFTWARE	ASP A:128 , FE A:337 , HOH A:505 , HOH A:506 , HOH A:508 , HOH A:513 , HOH A:1171	BINDING SITE FOR RESIDUE NA A 340
14	BC5	SOFTWARE	PHE A:142 , HOH A:522 , HOH A:523 , HOH A:524 , HOH A:525 , HOH A:1170	BINDING SITE FOR RESIDUE NA A 341
15	BC6	SOFTWARE	HOH A:1177 , HOH A:1178 , HOH A:1181 , HOH A:1183 , HOH A:1184 , HOH A:1185	BINDING SITE FOR RESIDUE NA A 342

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:319
 aligned with VPL2_PLEER | O94753 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:319
                                    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         
           VPL2_PLEER    31 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADP 349
               SCOP domains d3fm1a_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.ee...eee...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhee.hhhh................hhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------PEROXIDASE_---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm1 A   1 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPQVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADP 319
                                    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

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, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (VPL2_PLEER | O94753)

molecular function
	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.
	GO:0052750	reactive-black-5:hydrogen-peroxide oxidoreductase activity	Catalysis of the reaction: reactive black 5 + hydrogen peroxide = oxidized reactive black 5 + 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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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