PGOX_MYXXA
ID PGOX_MYXXA Reviewed; 471 AA.
AC P56601;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-1998, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=Protoporphyrinogen oxidase {ECO:0000303|PubMed:8621504};
DE Short=PPOX {ECO:0000303|PubMed:17046834};
DE EC=1.3.3.4 {ECO:0000269|PubMed:17046834};
GN Name=pgoX {ECO:0000303|PubMed:28123057}; Synonyms=hemY;
OS Myxococcus xanthus.
OC Bacteria; Proteobacteria; Deltaproteobacteria; Myxococcales;
OC Cystobacterineae; Myxococcaceae; Myxococcus.
OX NCBI_TaxID=34;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1372277; DOI=10.1101/gad.6.3.401;
RA Li S., Lee B.U., Shimkets L.J.;
RT "csgA expression entrains Myxococcus xanthus development.";
RL Genes Dev. 6:401-410(1992).
RN [2]
RP SEQUENCE REVISION TO C-TERMINUS.
RA Shimkets L.J.;
RL Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=8621504; DOI=10.1074/jbc.271.15.8714;
RA Dailey H.A., Dailey T.A.;
RT "Protoporphyrinogen oxidase of Myxococcus xanthus. Expression,
RT purification, and characterization of the cloned enzyme.";
RL J. Biol. Chem. 271:8714-8718(1996).
RN [4]
RP NOMENCLATURE, FUNCTION, AND REVIEW.
RX PubMed=28123057; DOI=10.1128/mmbr.00048-16;
RA Dailey H.A., Dailey T.A., Gerdes S., Jahn D., Jahn M., O'Brian M.R.,
RA Warren M.J.;
RT "Prokaryotic heme biosynthesis: multiple pathways to a common essential
RT product.";
RL Microbiol. Mol. Biol. Rev. 81:e00048-e00048(2017).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 4-471 IN COMPLEX WITH FAD AND
RP ACIFLUORFEN, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=17046834; DOI=10.1074/jbc.m606640200;
RA Corradi H.R., Corrigall A.V., Boix E., Mohan C.G., Sturrock E.D.,
RA Meissner P.N., Acharya K.R.;
RT "Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus
RT and its complex with the inhibitor acifluorfen.";
RL J. Biol. Chem. 281:38625-38633(2006).
CC -!- FUNCTION: Catalyzes the 6-electron oxidation of protoporphyrinogen-IX
CC to form protoporphyrin-IX (PubMed:8621504). Does not oxidize
CC coproporphyrinogen III (PubMed:8621504). Involved in the classical
CC protoporphyrin-dependent (PPD) heme b biosynthesis (PubMed:28123057).
CC {ECO:0000269|PubMed:8621504, ECO:0000303|PubMed:28123057}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 O2 + protoporphyrinogen IX = 3 H2O2 + protoporphyrin IX;
CC Xref=Rhea:RHEA:25576, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:57306, ChEBI:CHEBI:57307; EC=1.3.3.4;
CC Evidence={ECO:0000269|PubMed:8621504};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:25577;
CC Evidence={ECO:0000269|PubMed:8621504};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:8621504};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:8621504};
CC -!- ACTIVITY REGULATION: Strongly inhibited by acifluorfen.
CC {ECO:0000269|PubMed:8621504}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.6 uM for protoporphyrinogen {ECO:0000269|PubMed:8621504};
CC Note=kcat is 5.2 min(-1). {ECO:0000269|PubMed:8621504};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; protoporphyrin-IX from protoporphyrinogen-IX: step 1/1.
CC {ECO:0000305|PubMed:28123057}.
CC -!- SUBUNIT: Monomer (PubMed:17046834). Homodimer (PubMed:8621504).
CC {ECO:0000269|PubMed:17046834, ECO:0000269|PubMed:8621504}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17046834}. Cell
CC membrane {ECO:0000269|PubMed:17046834}. Note=Membrane-associated.
CC {ECO:0000269|PubMed:17046834}.
CC -!- SIMILARITY: Belongs to the protoporphyrinogen/coproporphyrinogen
CC oxidase family. Protoporphyrinogen oxidase subfamily. {ECO:0000305}.
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DR EMBL; L27429; AAM28643.1; -; Genomic_DNA.
DR EMBL; AF098938; AAD13609.1; -; Genomic_DNA.
DR RefSeq; WP_011551410.1; NZ_JABFNQ010000064.1.
DR PDB; 2IVD; X-ray; 2.30 A; A/B=4-471.
DR PDB; 2IVE; X-ray; 2.70 A; A/B=4-471.
DR PDBsum; 2IVD; -.
DR PDBsum; 2IVE; -.
DR AlphaFoldDB; P56601; -.
DR SMR; P56601; -.
DR DrugBank; DB07338; Acifluorfen.
DR GeneID; 41358739; -.
DR OMA; WFDQWFG; -.
DR BRENDA; 1.3.3.4; 3551.
DR SABIO-RK; P56601; -.
DR UniPathway; UPA00251; UER00324.
DR EvolutionaryTrace; P56601; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004729; F:oxygen-dependent protoporphyrinogen oxidase activity; IEA:InterPro.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR002937; Amino_oxidase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR004572; Protoporphyrinogen_oxidase.
DR Pfam; PF01593; Amino_oxidase; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR TIGRFAMs; TIGR00562; proto_IX_ox; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Cytoplasm; FAD; Flavoprotein;
KW Heme biosynthesis; Membrane; Oxidoreductase.
FT CHAIN 1..471
FT /note="Protoporphyrinogen oxidase"
FT /id="PRO_0000135267"
FT BINDING 16..21
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT BINDING 39..40
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT BINDING 47
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT BINDING 61..64
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT BINDING 251
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT BINDING 408
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 446..448
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:17046834"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 19..29
FT /evidence="ECO:0007829|PDB:2IVD"
FT TURN 30..32
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:2IVE"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 110..114
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 121..128
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 129..132
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 144..151
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 154..159
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 161..169
FT /evidence="ECO:0007829|PDB:2IVD"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 183..192
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 195..206
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 223..226
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 231..241
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 242..244
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 245..255
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 262..267
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 270..275
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 277..281
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 285..292
FT /evidence="ECO:0007829|PDB:2IVD"
FT TURN 293..295
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 297..304
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 311..318
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 328..332
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 343..346
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 347..350
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 360..367
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 372..376
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 379..394
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 401..410
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 419..431
FT /evidence="ECO:0007829|PDB:2IVD"
FT STRAND 436..438
FT /evidence="ECO:0007829|PDB:2IVD"
FT TURN 441..443
FT /evidence="ECO:0007829|PDB:2IVD"
FT HELIX 448..462
FT /evidence="ECO:0007829|PDB:2IVD"
SQ SEQUENCE 471 AA; 49388 MW; 2E9909D464F81515 CRC64;
MHHMPRTTGM NVAVVGGGIS GLAVAHHLRS RGTDAVLLES SARLGGAVGT HALAGYLVEQ
GPNSFLDREP ATRALAAALN LEGRIRAADP AAKRRYVYTR GRLRSVPASP PAFLASDILP
LGARLRVAGE LFSRRAPEGV DESLAAFGRR HLGHRATQVL LDAVQTGIYA GDVEQLSVAA
TFPMLVKMER EHRSLILGAI RAQKAQRQAA LPAGTAPKLS GALSTFDGGL QVLIDALAAS
LGDAAHVGAR VEGLAREDGG WRLIIEEHGR RAELSVAQVV LAAPAHATAK LLRPLDDALA
ALVAGIAYAP IAVVHLGFDA GTLPAPDGFG FLVPAEEQRR MLGAIHASTT FPFRAEGGRV
LYSCMVGGAR QPGLVEQDED ALAALAREEL KALAGVTARP SFTRVFRWPL GIPQYNLGHL
ERVAAIDAAL QRLPGLHLIG NAYKGVGLND CIRNAAQLAD ALVAGNTSHA P
