2W23 - JenaLib

Title :   STRUCTURE OF MUTANT W169Y OF PLEUROTUS ERYNGII VERSATILE PEROXIDASE (VP)

Authors :   F. J. Ruiz-Duenas, R. Pogni, M. Morales, S. Giansanti, M. J. Mate, A. Romero, M. J. Martinez, R. Basosi, A. T. Martinez

Date :   23 Oct 08 (Deposition) - 20 Jan 09 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Organic Radical, Protein Radicals, Lignin Degradation, Manganese Peroxidase, Electron Transfer, Hydrogen Peroxide, Iron, Heme, Calcium, Zymogen, Secreted, Manganese, Peroxidase, Glycoprotein, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. J. Ruiz-Duenas, R. Pogni, M. Morales, S. Giansanti, M. J. Mate, A. Romero, M. J. Martinez, R. Basosi, A. T. Martinez
Protein Radicals In Fungal Versatile Peroxidase: Catalytic Tryptophan Radical In Both Compound I And Compound Ii And Studies On W164Y, W164H, And W164S Variants.
J. Biol. Chem. V. 284 7986 2009
PubMed-ID: 19158088 | Reference-DOI: 10.1074/JBC.M808069200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:36 , HIS A:39 , GLU A:40 , LEU A:42 , PHE A:46 , PRO A:139 , GLU A:140 , PRO A:141 , LEU A:165 , 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 , HOH A:2046 , HOH A:2059 , HOH A:2358 , HOH A:2359 , HOH A:2360	BINDING SITE FOR RESIDUE HEM A1316
2	AC2	SOFTWARE	ASP A:48 , GLY A:60 , ASP A:62 , SER A:64 , HOH A:2065 , HOH A:2087	BINDING SITE FOR RESIDUE CA A1317
3	AC3	SOFTWARE	SER A:170 , ASP A:187 , THR A:189 , VAL A:192 , ASP A:194	BINDING SITE FOR RESIDUE CA A1318
4	AC4	SOFTWARE	HIS A:136 , GLU A:140 , ARG A:206 , HOH A:2168 , HOH A:2176 , HOH A:2361 , HOH A:2362 , HOH A:2363	BINDING SITE FOR RESIDUE SO4 A1319
5	AC5	SOFTWARE	PRO A:115 , SER A:188 , THR A:189 , VAL A:289 , GLY A:290 , HOH A:2364 , HOH A:2365 , HOH A:2366	BINDING SITE FOR RESIDUE GOL A1320

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
	(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:315
 aligned with VPL2_PLEER | O94753 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:315
                                    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 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVWLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPAL 345
               SCOP domains d2w23a_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------peroxidase-2w23A02 A:20-250                                                                                                                                                                                                            -DUF3415-2w23A01 A:252-315                                        Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee.........ee.........hhhhhhh...............ee........eehhhhhhh....hhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhee.hhhh................hhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PEROXIDASE_2---------------------------------------------------------------------------------------------------------------PEROXIDASE_------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w23 A   1 ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVYLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPAL 315
                                    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 (2, 2)

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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