HEMN_PARDP
ID HEMN_PARDP Reviewed; 451 AA.
AC Q51676; A1B354;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Oxygen-independent coproporphyrinogen III oxidase;
DE Short=CPO;
DE EC=1.3.98.3 {ECO:0000250|UniProtKB:P32131};
DE AltName: Full=Coproporphyrinogen III dehydrogenase;
DE Short=CPDH;
GN Name=hemN; OrderedLocusNames=Pden_1851;
OS Paracoccus denitrificans (strain Pd 1222).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=318586;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8809776; DOI=10.1111/j.1365-2958.1996.tb02644.x;
RA de Gier J.W., Schepper M., Reijnders W.N.M., van Dyck S.J., Slotboom D.J.,
RA Warne A., Saraste M., Krab K., Finel M., Stouthamer A.H.,
RA van Spanning R.J.M., der Oost J.;
RT "Structural and functional analysis of aa3-type and cbb3-type cytochrome c
RT oxidases of Paracoccus denitrificans reveals significant differences in
RT proton-pump design.";
RL Mol. Microbiol. 20:1247-1260(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pd 1222;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA Richardson P.;
RT "Complete sequence of chromosome 1 of Paracoccus denitrificans PD1222.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Involved in the heme biosynthesis. Catalyzes the anaerobic
CC oxidative decarboxylation of propionate groups of rings A and B of
CC coproporphyrinogen III to yield the vinyl groups in protoporphyrinogen
CC IX. {ECO:0000250|UniProtKB:P32131}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=coproporphyrinogen III + 2 S-adenosyl-L-methionine = 2 5'-
CC deoxyadenosine + 2 CO2 + 2 L-methionine + protoporphyrinogen IX;
CC Xref=Rhea:RHEA:15425, ChEBI:CHEBI:16526, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:57307, ChEBI:CHEBI:57309, ChEBI:CHEBI:57844,
CC ChEBI:CHEBI:59789; EC=1.3.98.3;
CC Evidence={ECO:0000250|UniProtKB:P32131};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P32131};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000250|UniProtKB:P32131};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (AdoMet
CC route): step 1/1.
CC -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:P32131}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P32131}.
CC -!- SIMILARITY: Belongs to the anaerobic coproporphyrinogen-III oxidase
CC family. {ECO:0000305}.
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DR EMBL; U34353; AAC44513.1; -; Genomic_DNA.
DR EMBL; CP000489; ABL69948.1; -; Genomic_DNA.
DR PIR; S77599; S77599.
DR RefSeq; WP_011748145.1; NC_008686.1.
DR AlphaFoldDB; Q51676; -.
DR SMR; Q51676; -.
DR STRING; 318586.Pden_1851; -.
DR PRIDE; Q51676; -.
DR EnsemblBacteria; ABL69948; ABL69948; Pden_1851.
DR KEGG; pde:Pden_1851; -.
DR eggNOG; COG0635; Bacteria.
DR HOGENOM; CLU_027579_3_0_5; -.
DR OMA; LMCNLEL; -.
DR UniPathway; UPA00251; UER00323.
DR Proteomes; UP000000361; Chromosome 1.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; ISS:UniProtKB.
DR GO; GO:0051989; F:coproporphyrinogen dehydrogenase activity; ISS:UniProtKB.
DR GO; GO:0004109; F:coproporphyrinogen oxidase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006779; P:porphyrin-containing compound biosynthetic process; ISS:UniProtKB.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; ISS:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR004558; Coprogen_oxidase_HemN.
DR InterPro; IPR034505; Coproporphyrinogen-III_oxidase.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR13932; PTHR13932; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000167; HemN; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00538; hemN; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Metal-binding; Oxidoreductase;
KW Porphyrin biosynthesis; Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..451
FT /note="Oxygen-independent coproporphyrinogen III oxidase"
FT /id="PRO_0000109945"
FT DOMAIN 45..278
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 54
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 60
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 64
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 66
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 111
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 112..113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 144
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 171
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 183
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 208
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 242
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P32131"
FT BINDING 328
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P32131"
SQ SEQUENCE 451 AA; 49848 MW; D424AA04E4B4519A CRC64;
MEQQSQLERL GLFDARVPRY TSYPTAPHFT PAVGEPVFRD WIAAIPAGAA ISLYMHVPFC
RRLCWFCACR TQGTQSDEPV RAYAKALLAE LDMLKSALAP GVRLSRLHWG GGTPTLMPAE
MMRLVAGAVL DAFPLAEGAE FSVEIDPNEI DEARMDALAE AGLNRASIGV QDFDPEIQKI
IGREQSFEVT KRAVDMIRDR GIASLNADIL YGLPHQDPHR IAESVQKLLA LSPDRVALYG
YAHVPWMAKR QVMIPSEALP DPHGRLRLFE TARELFLADG YDEIGIDHFA RPGDGLARAQ
KAGLLRRNFQ GYTDDRAEVL VGLGASSISR FPQGYAQNAP ATGAHLARIR DGRFSTTRGH
AFSAEDRWRS RMIEALMCDF EIRAEEFIRD HGFDAESLSR ILTPVAAHFG DMVDADASGL
RITPRGRPLT RMIARMFDGY DMAASGHSAA I
