ID Q31IC6_HYDCU Unreviewed; 460 AA.
AC Q31IC6;
DT 06-DEC-2005, integrated into UniProtKB/TrEMBL.
DT 06-DEC-2005, sequence version 1.
DT 27-MAR-2024, entry version 115.
DE RecName: Full=Coproporphyrinogen-III oxidase {ECO:0000256|PIRNR:PIRNR000167};
DE EC=1.3.98.3 {ECO:0000256|PIRNR:PIRNR000167};
GN OrderedLocusNames=Tcr_0501 {ECO:0000313|EMBL:ABB41097.1};
OS Hydrogenovibrio crunogenus (strain DSM 25203 / XCL-2) (Thiomicrospira
OS crunogena).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales;
OC Piscirickettsiaceae; Hydrogenovibrio.
OX NCBI_TaxID=317025 {ECO:0000313|EMBL:ABB41097.1};
RN [1] {ECO:0000313|EMBL:ABB41097.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=XCL-2 {ECO:0000313|EMBL:ABB41097.1};
RG US DOE Joint Genome Institute;
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 Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Lykidis A., Scott K.M., Sievert S., Kerfeld C.,
RA Freyermuth S., Dobrinski K., Boller A., Fitzpatrick K., Thoma P., Moore J.,
RA Richardson P.;
RT "Complete sequence of Thiomicrospira crunogena XCL-2.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
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:0000256|ARBA:ARBA00001496,
CC ECO:0000256|PIRNR:PIRNR000167};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|PIRNR:PIRNR000167,
CC ECO:0000256|PIRSR:PIRSR000167-2};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000256|PIRNR:PIRNR000167, ECO:0000256|PIRSR:PIRSR000167-2};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (AdoMet
CC route): step 1/1. {ECO:0000256|ARBA:ARBA00004785,
CC ECO:0000256|PIRNR:PIRNR000167}.
CC -!- SUBUNIT: Monomer. {ECO:0000256|ARBA:ARBA00011245}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496,
CC ECO:0000256|PIRNR:PIRNR000167}.
CC -!- SIMILARITY: Belongs to the anaerobic coproporphyrinogen-III oxidase
CC family. {ECO:0000256|ARBA:ARBA00005493, ECO:0000256|PIRNR:PIRNR000167}.
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DR EMBL; CP000109; ABB41097.1; -; Genomic_DNA.
DR AlphaFoldDB; Q31IC6; -.
DR STRING; 317025.Tcr_0501; -.
DR KEGG; tcx:Tcr_0501; -.
DR eggNOG; COG0635; Bacteria.
DR HOGENOM; CLU_027579_3_0_6; -.
DR OrthoDB; 9808022at2; -.
DR UniPathway; UPA00251; UER00323.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051989; F:coproporphyrinogen dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0004109; F:coproporphyrinogen oxidase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 1.10.10.920; -; 1.
DR Gene3D; 3.80.30.20; tm_1862 like domain; 1.
DR InterPro; IPR004558; Coprogen_oxidase_HemN.
DR InterPro; IPR034505; Coproporphyrinogen-III_oxidase.
DR InterPro; IPR006638; Elp3/MiaA/NifB-like_rSAM.
DR InterPro; IPR010723; HemN_C.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR023404; rSAM_horseshoe.
DR NCBIfam; TIGR00538; hemN; 1.
DR PANTHER; PTHR13932; COPROPORPHYRINIGEN III OXIDASE; 1.
DR PANTHER; PTHR13932:SF6; OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE; 1.
DR Pfam; PF06969; HemN_C; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000167; HemN; 1.
DR SFLD; SFLDG01065; anaerobic_coproporphyrinogen-I; 1.
DR SFLD; SFLDG01082; B12-binding_domain_containing; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|PIRNR:PIRNR000167};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|PIRNR:PIRNR000167};
KW Iron {ECO:0000256|PIRNR:PIRNR000167, ECO:0000256|PIRSR:PIRSR000167-2};
KW Iron-sulfur {ECO:0000256|PIRNR:PIRNR000167, ECO:0000256|PIRSR:PIRSR000167-
KW 2};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRNR:PIRNR000167};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000256|PIRNR:PIRNR000167};
KW Porphyrin biosynthesis {ECO:0000256|ARBA:ARBA00023244,
KW ECO:0000256|PIRNR:PIRNR000167};
KW S-adenosyl-L-methionine {ECO:0000256|PIRNR:PIRNR000167,
KW ECO:0000256|PIRSR:PIRSR000167-1}.
FT DOMAIN 48..292
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT BINDING 57
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 63
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-2"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-2"
FT BINDING 69..71
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-2"
FT BINDING 114
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 115..116
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 149
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 176
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 213
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 247
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
FT BINDING 333
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000167-1"
SQ SEQUENCE 460 AA; 52671 MW; 76DFBA5CCC41798F CRC64;
MEQSIRFDED LIKRYNQSGP RYTSYPTAVQ FDETFGVADY QAAAERSNAS DRNLSLYFHI
PFCDTVCFFC ACNKVWTRDR SKTTPYLARL YQEVEMQAKL FDSNRKVDQL HWGGGTPTFI
NMDEMRELMA VTRKHFNLHD DDSGEYSIEI DPREANKESV KLLRELGFNR MSLGVQDFDP
NVQKAVNRIQ TEAQTFEVLE GAREAGFMSV NVDLIYGLPH QTESGFMATL DKVLEVAPDR
FSIFNYAHMP SMFPTQKKMN EADMPSPDEK LAILHATTNR LLEAGYVYIG MDHFAKPDDE
LAVAQRNETL YRNFQGYSTH AECDLIGMGA TSISLINNTY AQNHKSLNDY YQAIDAGHLA
VFRGVELTED DELRRDVITR LISHFHLNFA SVEAQWGIVF KEYFEQEMNA LVPMIEDGLI
ELSDSDLYVT AAGRLLIRNI CMAFDAYLKQ GTQNRFSKVI
//
