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Title :   CRYSTALLIZATION OF A 45 KDA PEROXYGENASE- PEROXIDASE FROM THE MUSHROOM AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY SAD UTILIZING ONLY THE HAEM IRON

Authors :   K. Piontek, E. Strittmatter, R. Ullrich, D. A. Plattner, M. Hofrichter

Date :   26 Oct 12 (Deposition) - 23 Oct 13 (Release) - 01 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, Peroxidase/Peroxygenase, Unspecific/Aromatic Peroxygenase, Heme, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Piontek, E. Strittmatter, R. Ullrich, G. Grobe, M. J. Pecyna, M. Kluge, K. Scheibner, M. Hofrichter, D. A. Plattner
Structural Basis Of Substrate Conversion In A New Aromatic Peroxygenase: P450 Functionality With Benefits
J. Biol. Chem. V. 288 34767 2013
PubMed-ID: 24126915 | Reference-DOI: 10.1074/JBC.M113.514521
(for further references see the PDB file header)

Molecule 1 - AROMATIC PEROXYGENASE
	Chains	:	A, B
	EC Number	:	1.11.2.1
	Fragment	:	RESIDUES 47-371
	Organism Common	:	BLACK POPLAR MUSHROOM
	Organism Scientific	:	AGROCYBE AEGERITA
	Organism Taxid	:	5400
	Other Details	:	GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSMZ 22459
	Strain	:	TM-A1
	Synonym	:	AAPIIPH85, AAP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (9, 51)

No.	Name	Count	Type	Full Name
1	BMA	6	Ligand/Ion	BETA-D-MANNOSE
2	CL	4	Ligand/Ion	CHLORIDE ION
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	MAN	7	Ligand/Ion	ALPHA-D-MANNOSE
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	MZ0	2	Ligand/Ion	1H-IMIDAZOL-5-YLMETHANOL
7	NAG	21	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	SO4	6	Ligand/Ion	SULFATE ION
9	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (32, 32)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:36 , GLY A:38 , LEU A:39 , LEU A:67 , PHE A:69 , ALA A:77 , THR A:78 , PHE A:121 , GLU A:122 , GLY A:123 , SER A:126 , MET A:127 , THR A:128 , ARG A:189 , GLU A:196 , PHE A:199 , MG A:353 , MZ0 A:354 , HOH A:2152	BINDING SITE FOR RESIDUE HEM A 350
02	AC2	SOFTWARE	GLU A:122 , GLY A:123 , SER A:126 , HEM A:350 , HOH A:2151 , HOH A:2152	BINDING SITE FOR RESIDUE MG A 353
03	AC3	SOFTWARE	ALA A:77 , THR A:192 , GLU A:196 , PHE A:199 , HEM A:350 , HOH A:2096 , HOH A:2318	BINDING SITE FOR RESIDUE MZ0 A 354
04	AC4	SOFTWARE	PRO A:5 , VAL A:57 , TYR A:79 , ASP A:91 , THR A:306 , ASN A:307 , PHE A:310 , HOH A:2077 , HOH A:2297 , HOH A:2344	BINDING SITE FOR RESIDUE BMA A 501
05	AC5	SOFTWARE	THR A:297 , VAL A:298 , HOH A:2345	BINDING SITE FOR RESIDUE SO4 A1355
06	AC6	SOFTWARE	PRO A:8 , ASP A:70 , ASN A:71 , HOH A:2008	BINDING SITE FOR RESIDUE CL A1356
07	AC7	SOFTWARE	ARG A:97 , THR A:99 , ARG A:100 , HOH A:2118 , HOH A:2346	BINDING SITE FOR RESIDUE SO4 A1357
08	AC8	SOFTWARE	TYR A:151 , ARG A:154 , LYS A:171	BINDING SITE FOR RESIDUE SO4 A1358
09	AC9	SOFTWARE	PRO B:35 , CYS B:36 , PRO B:37 , LEU B:39 , VAL B:63 , LEU B:67 , ALA B:77 , THR B:78 , PHE B:121 , GLU B:122 , GLY B:123 , SER B:126 , MET B:127 , THR B:128 , ARG B:189 , GLU B:196 , PHE B:199 , LEU B:203 , MG B:353 , MZ0 B:354 , HOH B:2044 , HOH B:2126 , HOH B:2162	BINDING SITE FOR RESIDUE HEM B 350
10	BC1	SOFTWARE	GLU B:122 , GLY B:123 , SER B:126 , HEM B:350 , HOH B:2125 , HOH B:2126	BINDING SITE FOR RESIDUE MG B 353
11	BC2	SOFTWARE	ALA B:77 , THR B:192 , GLU B:196 , PHE B:199 , HEM B:350 , HOH B:2076 , HOH B:2266	BINDING SITE FOR RESIDUE MZ0 B 354
12	BC3	SOFTWARE	LEU B:88 , ILE B:89 , ASP B:91 , ALA B:303 , THR B:306 , HOH B:2092	BINDING SITE FOR RESIDUE BMA B 501
13	BC4	SOFTWARE	ASN B:182 , SER B:184 , VAL B:186 , ASP B:187 , ARG B:257 , HOH B:2169 , HOH B:2174 , HOH B:2285 , HOH B:2290	BINDING SITE FOR RESIDUE NAG B 511
14	BC5	SOFTWARE	ASN B:61 , CL B:1358	BINDING SITE FOR RESIDUE TRS B1355
15	BC6	SOFTWARE	ASP B:70 , ASN B:71 , PRO B:238 , HOH B:2008	BINDING SITE FOR RESIDUE CL B1356
16	BC7	SOFTWARE	ARG B:97 , HIS B:138 , HOH B:2038 , HOH B:2040 , HOH B:2291	BINDING SITE FOR RESIDUE SO4 B1357
17	BC8	SOFTWARE	GLY B:7 , TRS B:1355	BINDING SITE FOR RESIDUE CL B1358
18	BC9	SOFTWARE	LYS B:171 , MAN B:365 , MAN B:366 , MAN B:367 , HOH B:2274	BINDING SITE FOR RESIDUE SO4 B1359
19	CC1	SOFTWARE	ARG B:97 , LYS B:98 , THR B:99 , ARG B:100 , HOH B:2292	BINDING SITE FOR RESIDUE SO4 B1360
20	CC2	SOFTWARE	THR B:143	BINDING SITE FOR RESIDUE CL B1361
21	CC3	SOFTWARE	ASN A:11 , SER A:13 , HOH A:2020 , HOH A:2343	BINDING SITE FOR MONO-SACCHARIDE NAG A 411 BOUND TO ASN A 11
22	CC4	SOFTWARE	ASN A:141 , HOH A:2169 , HOH A:2320 , NAG B:401	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 361 THROUGH BMA A 363 BOUND TO ASN A 141
23	CC5	SOFTWARE	PHE A:155 , GLY A:156 , ASN A:161 , THR A:163 , GLN A:213 , HOH A:2181 , HOH A:2323 , HOH A:2327 , HOH A:2330 , HOH A:2331 , HOH A:2332 , HOH A:2333 , HOH A:2334 , GLU B:146 , ASP B:150 , ASN B:153 , CYS B:278 , ALA B:317 , CYS B:319	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 371 THROUGH MAN A 375 BOUND TO ASN A 161
24	CC6	SOFTWARE	PHE A:133 , ASN A:182 , HOH A:2161 , HOH A:2163 , HOH A:2335 , HOH A:2336 , HOH A:2337 , HOH A:2339	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 381 THROUGH BMA A 383 BOUND TO ASN A 182
25	CC7	SOFTWARE	ASN A:286	BINDING SITE FOR MONO-SACCHARIDE NAG A 391 BOUND TO ASN A 286
26	CC8	SOFTWARE	PRO A:294 , ASN A:295 , HOH A:2340 , HOH A:2341 , HOH A:2342	BINDING SITE FOR MONO-SACCHARIDE NAG A 401 BOUND TO ASN A 295
27	CC9	SOFTWARE	ASN B:11 , SER B:13 , HOH B:2288	BINDING SITE FOR MONO-SACCHARIDE NAG B 411 BOUND TO ASN B 11
28	DC1	SOFTWARE	LEU B:16 , PHE B:133 , PHE B:134 , ASN B:141 , LYS B:171 , GLN B:174 , ASP B:175 , THR B:179 , PRO B:181 , ASP B:231 , SO4 B:1359 , HOH B:2145 , HOH B:2163 , HOH B:2200 , HOH B:2218 , HOH B:2267 , HOH B:2268 , HOH B:2269 , HOH B:2270 , HOH B:2271 , HOH B:2272 , HOH B:2273 , HOH B:2274 , HOH B:2275 , HOH B:2276 , HOH B:2277 , HOH B:2278 , HOH B:2279 , HOH B:2280 , HOH B:2281 , HOH B:2282	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 361 THROUGH MAN B 368 BOUND TO ASN B 141
29	DC2	SOFTWARE	CYS A:278 , GLU A:282 , ALA A:317 , CYS A:319 , HOH A:2313 , PHE B:155 , GLY B:156 , ASN B:161 , THR B:163 , GLN B:213 , HOH B:2153 , HOH B:2157	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 371 THROUGH NAG B 372 BOUND TO ASN B 161
30	DC3	SOFTWARE	PHE B:133 , ASN B:182 , HOH B:2284 , HOH B:2286	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 381 THROUGH NAG B 382 BOUND TO ASN B 182
31	DC4	SOFTWARE	HOH A:2329 , GLU B:282 , ASN B:286 , VAL B:322 , HOH B:2262	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 391 THROUGH NAG B 392 BOUND TO ASN B 286
32	DC5	SOFTWARE	BMA A:363 , PRO B:294 , ASN B:295 , HOH B:2240	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 401 THROUGH NAG B 402 BOUND TO ASN B 295

Asymmetric/Biological Unit

No.	Residues
1	A:278	-	A:319
2	B:278	-	B:319

Asymmetric/Biological Unit

No.	Residues
1	Pro A:108	-	Pro A:109
2	Pro B:108	-	Pro B:109

(no "SAP(SNP)/Variant" information available for 2YOR)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEME_HALOPEROXIDASE	PS51405	Heme haloperoxidase family profile.	APO1_AGRAE	63-291	2	A:20-248 B:20-248

(no "Exon" information available for 2YOR)

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)
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Chain A from PDB  Type:PROTEIN  Length:324
 aligned with APO1_AGRAE | B9W4V6 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:324
                                    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    
           APO1_AGRAE    48 PPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGYLPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDLLSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNNHDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPNFSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSRMPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSSDFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAAGCTQVFPYGRD 371
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............................hhhhhhhhhh.......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......ee....hhhhh...........................hhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh................hhhhhhhhh....ee........ee........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------HEME_HALOPEROXIDASE  PDB: A:20-248 UniProt: 63-291                                                                                                                                                                                   -------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yor A   5 PPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGYLPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDLLSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNNHDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPNFSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSRMPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSSDFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAAGCTQVFPYGRD 328
                                    14        24        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

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with APO1_AGRAE | B9W4V6 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:324
                                    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       346       356       366    
           APO1_AGRAE    47 LPPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGYLPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDLLSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNNHDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPNFSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSRMPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSSDFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAAGCTQVFPYGR 370
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................................hhhhhhhhhh.......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......ee....hhhhh...........................hhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.................hhhhhhhhh....ee........ee........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------HEME_HALOPEROXIDASE  PDB: B:20-248 UniProt: 63-291                                                                                                                                                                                   ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yor B   4 LPPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGYLPRNGVATPVQIINAVQEGLNFDNQAAVFATYAAHLVDGNLITDLLSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNNHDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPNFSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSRMPDDFFRAPSPRSGTGVEVVIQAHPMQPGRNVGKINSYTVDPTSSDFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFFFQGVAAGCTQVFPYGR 327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323

Legend:		→ Mismatch	(orange background)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2YOR)

(no "CATH Domain" information available for 2YOR)

(no "Pfam Domain" information available for 2YOR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (APO1_AGRAE | B9W4V6)

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.
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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	APO1_AGRAE \| B9W4V6	:	2yp1

2yp1	CRYSTALLIZATION OF A 45 KDA PEROXYGENASE- PEROXIDASE FROM THE MUSHROOM AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY SAD UTILIZING ONLY THE HAEM IRON

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 51)

Sites (32, 32)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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Gene Ontology (7, 7)

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