CHDC_LISMO
ID CHDC_LISMO Reviewed; 251 AA.
AC Q8Y5F1;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Coproheme decarboxylase {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000303|PubMed:29536725};
DE EC=1.3.98.5 {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000269|PubMed:27758026, ECO:0000269|PubMed:29536725, ECO:0000269|PubMed:31423350};
DE AltName: Full=Coproheme III oxidative decarboxylase {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000305};
DE AltName: Full=Hydrogen peroxide-dependent heme synthase {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000305};
DE AltName: Full=LmCld {ECO:0000303|PubMed:25602700};
GN Name=chdC {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000303|PubMed:29536725};
GN Synonyms=hemQ {ECO:0000303|PubMed:25602700}; OrderedLocusNames=lmo2113;
OS Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Listeriaceae; Listeria.
OX NCBI_TaxID=169963;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-679 / EGD-e;
RX PubMed=11679669; DOI=10.1126/science.1063447;
RA Glaser P., Frangeul L., Buchrieser C., Rusniok C., Amend A., Baquero F.,
RA Berche P., Bloecker H., Brandt P., Chakraborty T., Charbit A.,
RA Chetouani F., Couve E., de Daruvar A., Dehoux P., Domann E.,
RA Dominguez-Bernal G., Duchaud E., Durant L., Dussurget O., Entian K.-D.,
RA Fsihi H., Garcia-del Portillo F., Garrido P., Gautier L., Goebel W.,
RA Gomez-Lopez N., Hain T., Hauf J., Jackson D., Jones L.-M., Kaerst U.,
RA Kreft J., Kuhn M., Kunst F., Kurapkat G., Madueno E., Maitournam A.,
RA Mata Vicente J., Ng E., Nedjari H., Nordsiek G., Novella S., de Pablos B.,
RA Perez-Diaz J.-C., Purcell R., Remmel B., Rose M., Schlueter T., Simoes N.,
RA Tierrez A., Vazquez-Boland J.-A., Voss H., Wehland J., Cossart P.;
RT "Comparative genomics of Listeria species.";
RL Science 294:849-852(2001).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF MET-149 AND GLN-187.
RX PubMed=29536725; DOI=10.1021/acs.biochem.8b00186;
RA Milazzo L., Hofbauer S., Howes B.D., Gabler T., Furtmueller P.G.,
RA Obinger C., Smulevich G.;
RT "Insights into the active site of coproheme decarboxylase from Listeria
RT monocytogenes.";
RL Biochemistry 57:2044-2057(2018).
RN [3] {ECO:0007744|PDB:4WWS}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), COFACTOR, AND SUBUNIT.
RX PubMed=25602700; DOI=10.1016/j.abb.2015.01.010;
RA Hofbauer S., Hagmuller A., Schaffner I., Mlynek G., Krutzler M.,
RA Stadlmayr G., Pirker K.F., Obinger C., Daims H., Djinovic-Carugo K.,
RA Furtmuller P.G.;
RT "Structure and heme-binding properties of HemQ (chlorite dismutase-like
RT protein) from Listeria monocytogenes.";
RL Arch. Biochem. Biophys. 574:36-48(2015).
RN [4] {ECO:0007744|PDB:5LOQ}
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 2-251 IN COMPLEX WITH
RP FE-COPROPORPHYRIN III, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, AND SUBUNIT.
RX PubMed=27758026; DOI=10.1111/febs.13930;
RA Hofbauer S., Mlynek G., Milazzo L., Puhringer D., Maresch D., Schaffner I.,
RA Furtmuller P.G., Smulevich G., Djinovic-Carugo K., Obinger C.;
RT "Hydrogen peroxide-mediated conversion of coproheme to heme b by HemQ-
RT lessons from the first crystal structure and kinetic studies.";
RL FEBS J. 283:4386-4401(2016).
RN [5] {ECO:0007744|PDB:6FXJ, ECO:0007744|PDB:6FXQ}
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 2-251, FUNCTION, CATALYTIC
RP ACTIVITY, REACTION MECHANISM, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF
RP TYR-147.
RX PubMed=31423350; DOI=10.1021/acscatal.9b00963;
RA Milazzo L., Gabler T., Puhringer D., Jandova Z., Maresch D., Michlits H.,
RA Pfanzagl V., Djinovic-Carugo K., Oostenbrink C., Furtmuller P.G.,
RA Obinger C., Smulevich G., Hofbauer S.;
RT "Redox cofactor rotates during its stepwise decarboxylation: molecular
RT mechanism of conversion of coproheme to heme b.";
RL ACS Catal. 9:6766-6782(2019).
CC -!- FUNCTION: Involved in coproporphyrin-dependent heme b biosynthesis
CC (PubMed:27758026, PubMed:31423350). Catalyzes the decarboxylation of
CC Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last
CC step of the pathway (PubMed:27758026, PubMed:31423350,
CC PubMed:29536725). The reaction occurs in a stepwise manner with a
CC three-propionate intermediate (PubMed:27758026, PubMed:31423350).
CC {ECO:0000269|PubMed:27758026, ECO:0000269|PubMed:29536725,
CC ECO:0000269|PubMed:31423350}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Fe-coproporphyrin III + 2 H(+) + 2 H2O2 = 2 CO2 + 4 H2O + heme
CC b; Xref=Rhea:RHEA:56516, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:16526, ChEBI:CHEBI:60344,
CC ChEBI:CHEBI:68438; EC=1.3.98.5; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01442, ECO:0000269|PubMed:27758026,
CC ECO:0000269|PubMed:29536725, ECO:0000269|PubMed:31423350};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:56517;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000269|PubMed:27758026, ECO:0000269|PubMed:31423350};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Fe-coproporphyrin III + H(+) + H2O2 = CO2 + 2 H2O +
CC harderoheme III; Xref=Rhea:RHEA:57940, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16240, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:68438, ChEBI:CHEBI:142463; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01442, ECO:0000269|PubMed:31423350};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:57941;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000269|PubMed:27758026, ECO:0000269|PubMed:31423350};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + H2O2 + harderoheme III = CO2 + 2 H2O + heme b;
CC Xref=Rhea:RHEA:57944, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:16526, ChEBI:CHEBI:60344,
CC ChEBI:CHEBI:142463; Evidence={ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000269|PubMed:31423350};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:57945;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000269|PubMed:27758026, ECO:0000269|PubMed:31423350};
CC -!- COFACTOR:
CC Name=Fe-coproporphyrin III; Xref=ChEBI:CHEBI:68438;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000269|PubMed:27758026};
CC Note=Fe-coproporphyrin III acts as both substrate and redox cofactor
CC (PubMed:27758026). Was originally thought to use heme as a cofactor
CC (PubMed:25602700). {ECO:0000269|PubMed:25602700,
CC ECO:0000269|PubMed:27758026};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=37.1 uM for H(2)O(2) {ECO:0000269|PubMed:27758026};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoheme
CC biosynthesis. {ECO:0000255|HAMAP-Rule:MF_01442,
CC ECO:0000305|PubMed:27758026}.
CC -!- SUBUNIT: Homopentamer (PubMed:25602700, PubMed:27758026,
CC PubMed:31423350). Homohexamer in solution (PubMed:25602700).
CC {ECO:0000269|PubMed:25602700, ECO:0000269|PubMed:27758026,
CC ECO:0000269|PubMed:31423350}.
CC -!- SIMILARITY: Belongs to the ChdC family. Type 1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01442, ECO:0000305}.
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DR EMBL; AL591982; CAD00191.1; -; Genomic_DNA.
DR PIR; AI1338; AI1338.
DR RefSeq; NP_465637.1; NC_003210.1.
DR RefSeq; WP_003722373.1; NZ_CP023861.1.
DR PDB; 4WWS; X-ray; 2.00 A; A/B/C/D/E=1-251.
DR PDB; 5LOQ; X-ray; 1.69 A; A/B/C/D/E=2-251.
DR PDB; 6FXJ; X-ray; 1.79 A; A/B/C/D/E=1-251.
DR PDB; 6FXQ; X-ray; 1.69 A; A/B/C/D/E=2-251.
DR PDBsum; 4WWS; -.
DR PDBsum; 5LOQ; -.
DR PDBsum; 6FXJ; -.
DR PDBsum; 6FXQ; -.
DR AlphaFoldDB; Q8Y5F1; -.
DR SMR; Q8Y5F1; -.
DR STRING; 169963.lmo2113; -.
DR PaxDb; Q8Y5F1; -.
DR EnsemblBacteria; CAD00191; CAD00191; CAD00191.
DR GeneID; 984744; -.
DR KEGG; lmo:lmo2113; -.
DR PATRIC; fig|169963.11.peg.2165; -.
DR eggNOG; COG3253; Bacteria.
DR HOGENOM; CLU_063226_1_0_9; -.
DR OMA; RYTMWSV; -.
DR PhylomeDB; Q8Y5F1; -.
DR BioCyc; LMON169963:LMO2113-MON; -.
DR BRENDA; 1.3.98.5; 3045.
DR UniPathway; UPA00252; -.
DR Proteomes; UP000000817; Chromosome.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004601; F:peroxidase activity; IEA:InterPro.
DR GO; GO:0006783; P:heme biosynthetic process; IEA:UniProtKB-KW.
DR HAMAP; MF_01442; Coproheme_decarbox_1; 1.
DR InterPro; IPR031332; CHDC.
DR InterPro; IPR010644; ChdC/CLD.
DR InterPro; IPR011008; Dimeric_a/b-barrel.
DR PANTHER; PTHR36843; PTHR36843; 1.
DR Pfam; PF06778; Chlor_dismutase; 1.
DR SUPFAM; SSF54909; SSF54909; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Heme; Heme biosynthesis; Iron; Metal-binding; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..251
FT /note="Coproheme decarboxylase"
FT /id="PRO_0000294042"
FT ACT_SITE 147
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000305|PubMed:31423350"
FT BINDING 133
FT /ligand="Fe-coproporphyrin III"
FT /ligand_id="ChEBI:CHEBI:68438"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000269|PubMed:27758026, ECO:0007744|PDB:5LOQ"
FT BINDING 147..151
FT /ligand="Fe-coproporphyrin III"
FT /ligand_id="ChEBI:CHEBI:68438"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000269|PubMed:27758026, ECO:0007744|PDB:5LOQ"
FT BINDING 174
FT /ligand="Fe-coproporphyrin III"
FT /ligand_id="ChEBI:CHEBI:68438"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000269|PubMed:27758026, ECO:0007744|PDB:5LOQ"
FT BINDING 187
FT /ligand="Fe-coproporphyrin III"
FT /ligand_id="ChEBI:CHEBI:68438"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000269|PubMed:27758026, ECO:0007744|PDB:5LOQ"
FT BINDING 225
FT /ligand="Fe-coproporphyrin III"
FT /ligand_id="ChEBI:CHEBI:68438"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01442,
FT ECO:0000269|PubMed:27758026, ECO:0007744|PDB:5LOQ"
FT MUTAGEN 147
FT /note="Y->A,H: Loss of activity."
FT /evidence="ECO:0000269|PubMed:31423350"
FT MUTAGEN 149
FT /note="M->A: Slight decrease in activity."
FT /evidence="ECO:0000269|PubMed:29536725"
FT MUTAGEN 187
FT /note="Q->A: Alters Fe-coproporphyrin III binding. Does not
FT affect kcat, but the reaction is less efficient and a
FT higher excess of hydrogen peroxide is needed."
FT /evidence="ECO:0000269|PubMed:29536725"
FT STRAND 7..20
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 22..26
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 30..52
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 55..63
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:6FXJ"
FT STRAND 69..78
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 79..90
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 93..97
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 98..114
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 120..122
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 128..134
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 142..151
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 164..179
FT /evidence="ECO:0007829|PDB:5LOQ"
FT TURN 180..184
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:5LOQ"
FT TURN 193..195
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 196..208
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 210..220
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 223..226
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:5LOQ"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:5LOQ"
FT HELIX 242..248
FT /evidence="ECO:0007829|PDB:5LOQ"
SQ SEQUENCE 251 AA; 28852 MW; D355A6F544402061 CRC64;
MNEAVKTLDG WFCLHDFRSI DWAAWRELNP GNQELMLNEL SHFLSDMEIT KNIGEGEHTI
YSILGQKADL VFFTLRDSLE ALNEVENRFN KLAIADYLLP TYSYISVVEL SNYLASHMAG
GDDPYQNKGV RARLYPALPP KKHICFYPMS KKRDGADNWY MLPMEERQQL IRDHGLIGRS
YAGKVQQIIG GSIGFDDYEW GVTLFSDDAL EFKRIVTEMR FDEASARYAE FGSFFIGNLL
LSEQLSKLFT I
