DYP2_AMYS7
ID DYP2_AMYS7 Reviewed; 464 AA.
AC K7N5M8;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2015, sequence version 2.
DT 03-AUG-2022, entry version 30.
DE RecName: Full=Multifunctional dye peroxidase DyP2 {ECO:0000303|PubMed:23054399};
DE EC=1.11.1.16 {ECO:0000269|PubMed:23054399};
DE EC=1.11.1.19 {ECO:0000269|PubMed:23054399};
DE EC=1.11.1.7 {ECO:0000269|PubMed:23054399};
DE AltName: Full=Dye decolorizing peroxidase 2 {ECO:0000303|PubMed:23054399};
DE Short=DyP2 {ECO:0000303|PubMed:23054399};
DE AltName: Full=Manganese peroxidase {ECO:0000303|PubMed:23054399};
GN Name=dyp2 {ECO:0000303|PubMed:23054399};
OS Amycolatopsis sp. (strain ATCC 39116 / 75iv2).
OC Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
OC Amycolatopsis; unclassified Amycolatopsis.
OX NCBI_TaxID=385957;
RN [1]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH HEME AND MANGANESE,
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC 39116 / 75iv2;
RX PubMed=23054399; DOI=10.1021/cb300383y;
RA Brown M.E., Barros T., Chang M.C.;
RT "Identification and characterization of a multifunctional dye peroxidase
RT from a lignin-reactive bacterium.";
RL ACS Chem. Biol. 7:2074-2081(2012).
CC -!- FUNCTION: Displays both high peroxidase and manganese peroxidase
CC activity. Is likely involved in lignin degradation. Also has a Mn-
CC dependent oxidase mode of action that expands its substrate scope in
CC vitro; is thus able to catalyze the O(2)- and Mn-dependent oxidative
CC decarboxylation of 4-methoxymandelate to anisaldehyde.
CC {ECO:0000269|PubMed:23054399}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-
CC diol + H2O2 = glycolaldehyde + guaiacol + H2O + vanillin;
CC Xref=Rhea:RHEA:22396, ChEBI:CHEBI:15377, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:17071, ChEBI:CHEBI:18346, ChEBI:CHEBI:28591,
CC ChEBI:CHEBI:53650; EC=1.11.1.16;
CC Evidence={ECO:0000269|PubMed:23054399};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H(+) + H2O2 + 2 Mn(2+) = 2 H2O + 2 Mn(3+);
CC Xref=Rhea:RHEA:22776, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:29035, ChEBI:CHEBI:29041;
CC EC=1.11.1.16; Evidence={ECO:0000269|PubMed:23054399};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2
CC H2O; Xref=Rhea:RHEA:56136, ChEBI:CHEBI:15377, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:139520, ChEBI:CHEBI:139521; EC=1.11.1.7;
CC Evidence={ECO:0000269|PubMed:23054399};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 H2O2 + Reactive Blue 5 = 2,2'-disulfonyl azobenzene + 3-[(4-
CC amino-6-chloro-1,3,5-triazin-2-yl)amino]benzenesulfonate + 2 H(+) + 2
CC H2O + phthalate; Xref=Rhea:RHEA:28086, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16240, ChEBI:CHEBI:17563,
CC ChEBI:CHEBI:63950, ChEBI:CHEBI:63955, ChEBI:CHEBI:64278;
CC EC=1.11.1.19; Evidence={ECO:0000269|PubMed:23054399};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:23054399};
CC Note=Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit.
CC {ECO:0000269|PubMed:23054399};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23054399};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13 uM for ABTS {ECO:0000269|PubMed:23054399};
CC KM=48 uM for Reactive Blue 5 {ECO:0000269|PubMed:23054399};
CC KM=2.4 uM for Reactive Black 5 {ECO:0000269|PubMed:23054399};
CC KM=1.2 mM for 2,4-dichlorophenol {ECO:0000269|PubMed:23054399};
CC KM=210 uM for Mn(2+) (when assaying manganese peroxidase activity)
CC {ECO:0000269|PubMed:23054399};
CC KM=760 uM for Mn(2+) (when assaying 4-methoxymandelate oxidase
CC activity) {ECO:0000269|PubMed:23054399};
CC Note=kcat is 87 sec(-1) for peroxidase activity with ABTS as
CC substrate. kcat is 34 sec(-1) for peroxidase activity with Reactive
CC Blue 5 as substrate. kcat is 0.38 sec(-1) for peroxidase activity
CC with Reactive Black 5 as substrate. kcat is 68 sec(-1) for peroxidase
CC activity with 2,4-dichlorophenol as substrate. kcat is 24 sec(-1) for
CC manganese peroxidase activity.;
CC pH dependence:
CC Optimum pH is 4.5 for the H(2)O(2)-dependent oxidation of Reactive
CC Blue 5, and 5.0 for the O(2)-dependent oxidation of 4-
CC methoxymandelate. {ECO:0000269|PubMed:23054399};
CC -!- SUBUNIT: Exists both as a monomeric and oligomeric species in solution;
CC the monomeric form contains no bound heme cofactor and is inactive.
CC {ECO:0000269|PubMed:23054399}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305|PubMed:23054399}.
CC Note=Although no signal sequence is found, the secretory machinery for
CC actinomycetes is not fully characterized, and the low pH optimum for
CC DyP2 along with the observation that many DyPs have been isolated from
CC the secreted protein fraction imply that DyP2 could be secreted and
CC still possibly play a role in extracellular oxidation chemistry
CC (PubMed:23054399).
CC -!- SIMILARITY: Belongs to the DyP-type peroxidase family. {ECO:0000305}.
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DR RefSeq; WP_020421762.1; NZ_AFWY03000046.1.
DR PDB; 4G2C; X-ray; 2.25 A; A/B=1-464.
DR PDBsum; 4G2C; -.
DR AlphaFoldDB; K7N5M8; -.
DR SMR; K7N5M8; -.
DR BRENDA; 1.11.1.19; 316.
DR SABIO-RK; K7N5M8; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0020037; F:heme binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0016689; F:manganese peroxidase activity; IEA:RHEA.
DR GO; GO:0004601; F:peroxidase activity; IDA:UniProtKB.
DR GO; GO:0052750; F:reactive-black-5:hydrogen-peroxide oxidoreductase activity; IEA:UniProtKB-EC.
DR InterPro; IPR011008; Dimeric_a/b-barrel.
DR InterPro; IPR006314; Dyp_peroxidase.
DR SUPFAM; SSF54909; SSF54909; 1.
DR TIGRFAMs; TIGR01413; Dyp_perox_fam; 1.
DR PROSITE; PS51404; DYP_PEROXIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Heme; Iron; Manganese; Metal-binding; Oxidoreductase;
KW Peroxidase; Secreted.
FT CHAIN 1..464
FT /note="Multifunctional dye peroxidase DyP2"
FT /id="PRO_0000433002"
FT ACT_SITE 203
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q47KB1"
FT BINDING 258
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:23054399"
FT BINDING 273
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:23054399"
FT BINDING 284
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:23054399"
FT BINDING 321
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:23054399,
FT ECO:0007744|PDB:4G2C"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 16..24
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 36..46
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 48..59
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 65..78
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 92..98
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 106..110
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 129..132
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 137..145
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 146..159
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 164..173
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 199..208
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 234..236
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 238..249
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 251..264
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 269..273
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 274..280
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 298..301
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 321..325
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 336..339
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 340..342
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 349..351
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 364..366
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 373..381
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 383..386
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 387..392
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 393..396
FT /evidence="ECO:0007829|PDB:4G2C"
FT TURN 413..415
FT /evidence="ECO:0007829|PDB:4G2C"
FT STRAND 445..455
FT /evidence="ECO:0007829|PDB:4G2C"
FT HELIX 458..462
FT /evidence="ECO:0007829|PDB:4G2C"
SQ SEQUENCE 464 AA; 50225 MW; C0704BAFE16055FE CRC64;
MPVDLSTTLS WKSATGEAAT MLDELQPNIL KAHVRDRLTV LFLGFGDAAE ARTFLNGLSG
LMKSARTHLQ EVEAHKLTKA VGTPYLGVGL TAHGYATLGV TAPADPSFTA GAKAAVEKLA
DPAVTEWEGH YQQTIDAVLL LGDATAGPVR TLRRQVEALR PASVTVVGEE SGLGLANANG
DGIEHFGYVD GRSQPLFLTE DVDAERDTTD GVNDWDPSAP LEQVLVPDPA APDPTVHFGS
YFVFRKLEQN VRLFKEAERD LAHDLGLRGE DRERAGAMLV GRFEDGTPLT AQSAPGSHHP
VGNDFSYDSD KLGQKCPFHA HIRKTNPRGS GGAEAPEEER KHLMARRGQT YGRRHDDPNA
DLPPRLRPAK DVGLLFMAFN SNLGNQFEFT QQIWANNPAF PFPPDGSQPG LDPVIGQGAR
APQKYAPEWG HNNVAEATDP IPQAVTMKGG EYFFMPSLAF LRSL
