HEMN_ECOLI
ID HEMN_ECOLI Reviewed; 457 AA.
AC P32131; P76772; Q2M8G4;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 4.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=Oxygen-independent coproporphyrinogen III oxidase;
DE Short=CPO;
DE EC=1.3.98.3 {ECO:0000269|PubMed:12114526};
DE AltName: Full=Coproporphyrinogen III dehydrogenase;
DE Short=CPDH;
GN Name=hemN; Synonyms=yihJ; OrderedLocusNames=b3867, JW3838;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Wachi M., Hamano-Takaku F., Nagano K., Kobayashi M., Yukawa H., Nagai K.;
RT "Sequence of the downstream flanking region of the glnALG genes of
RT Escherichia coli.";
RL Submitted (JUN-1993) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=K12;
RX PubMed=7768836; DOI=10.1128/jb.177.11.3326-3331.1995;
RA Troup B., Hungerer C., Jahn D.;
RT "Cloning and characterization of the Escherichia coli hemN gene encoding
RT the oxygen-independent coproporphyrinogen III oxidase.";
RL J. Bacteriol. 177:3326-3331(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8346018; DOI=10.1093/nar/21.15.3391;
RA Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome. III. DNA sequence of the region
RT from 87.2 to 89.2 minutes.";
RL Nucleic Acids Res. 21:3391-3398(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP PROTEIN SEQUENCE OF 1-4, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF
RP TYR-56; HIS-58; CYS-62; CYS-66; PHE-68; CYS-69; CYS-71; GLY-111 AND
RP GLY-113, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION, COFACTOR, ACTIVITY
RP REGULATION, REACTION MECHANISM, AND SUBUNIT.
RX PubMed=12114526; DOI=10.1074/jbc.m205247200;
RA Layer G., Verfuerth K., Mahlitz E., Jahn D.;
RT "Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia
RT coli.";
RL J. Biol. Chem. 277:34136-34142(2002).
RN [7]
RP MUTAGENESIS OF TYR-56; GLU-145; PHE-310; GLN-311 AND ILE-329.
RX PubMed=15967800; DOI=10.1074/jbc.m501275200;
RA Layer G., Grage K., Teschner T., Schuenemann V., Breckau D., Masoumi A.,
RA Jahn M., Heathcote P., Trautwein A.X., Jahn D.;
RT "Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN:
RT functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-
RT methionines.";
RL J. Biol. Chem. 280:29038-29046(2005).
RN [8]
RP REACTION MECHANISM.
RX PubMed=16606627; DOI=10.1074/jbc.m512628200;
RA Layer G., Pierik A.J., Trost M., Rigby S.E., Leech H.K., Grage K.,
RA Breckau D., Astner I., Jansch L., Heathcote P., Warren M.J., Heinz D.W.,
RA Jahn D.;
RT "The substrate radical of Escherichia coli oxygen-independent
RT coproporphyrinogen III oxidase HemN.";
RL J. Biol. Chem. 281:15727-15734(2006).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH 4FE-4S AND
RP S-ADENOSYL-L-METHIONINE, CATALYTIC MECHANISM, COFACTOR, AND SUBUNIT.
RX PubMed=14633981; DOI=10.1093/emboj/cdg598;
RA Layer G., Moser J., Heinz D.W., Jahn D., Schubert W.-D.;
RT "Crystal structure of coproporphyrinogen III oxidase reveals cofactor
RT geometry of Radical SAM enzymes.";
RL EMBO J. 22:6214-6224(2003).
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. It can use NAD or NADP, but NAD is preferred.
CC {ECO:0000269|PubMed:12114526, ECO:0000269|PubMed:7768836}.
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:0000269|PubMed:12114526};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:12114526, ECO:0000269|PubMed:14633981};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:12114526, ECO:0000269|PubMed:14633981};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:12114526}.
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:0000269|PubMed:12114526,
CC ECO:0000269|PubMed:14633981}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12114526}.
CC -!- MISCELLANEOUS: The structure carries two S-adenosyl-L-methionine
CC binding sites with only one binding to the iron-sulfur cluster.
CC {ECO:0000305|PubMed:14633981}.
CC -!- SIMILARITY: Belongs to the anaerobic coproporphyrinogen-III oxidase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB03001.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; D16509; BAA03961.1; -; Genomic_DNA.
DR EMBL; X82073; CAA57578.1; -; Genomic_DNA.
DR EMBL; L19201; AAB03001.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76864.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77442.1; -; Genomic_DNA.
DR RefSeq; NP_418303.2; NC_000913.3.
DR RefSeq; WP_000116090.1; NZ_STEB01000017.1.
DR PDB; 1OLT; X-ray; 2.07 A; A=1-457.
DR PDBsum; 1OLT; -.
DR AlphaFoldDB; P32131; -.
DR SMR; P32131; -.
DR BioGRID; 4262627; 13.
DR BioGRID; 852659; 2.
DR DIP; DIP-9887N; -.
DR IntAct; P32131; 7.
DR STRING; 511145.b3867; -.
DR jPOST; P32131; -.
DR PaxDb; P32131; -.
DR PRIDE; P32131; -.
DR EnsemblBacteria; AAC76864; AAC76864; b3867.
DR EnsemblBacteria; BAE77442; BAE77442; BAE77442.
DR GeneID; 66672228; -.
DR GeneID; 948362; -.
DR KEGG; ecj:JW3838; -.
DR KEGG; eco:b3867; -.
DR PATRIC; fig|1411691.4.peg.2845; -.
DR EchoBASE; EB1782; -.
DR eggNOG; COG0635; Bacteria.
DR HOGENOM; CLU_027579_3_0_6; -.
DR InParanoid; P32131; -.
DR OMA; LMCNLEL; -.
DR PhylomeDB; P32131; -.
DR BioCyc; EcoCyc:HEMN-MON; -.
DR BioCyc; MetaCyc:HEMN-MON; -.
DR BRENDA; 1.3.98.3; 2026.
DR UniPathway; UPA00251; UER00323.
DR EvolutionaryTrace; P32131; -.
DR PRO; PR:P32131; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0051989; F:coproporphyrinogen dehydrogenase activity; IDA:EcoCyc.
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; IBA:GO_Central.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IDA: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; IPR010723; HemN_C.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR13932; PTHR13932; 1.
DR Pfam; PF06969; HemN_C; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000167; HemN; 1.
DR SFLD; SFLDF00277; oxygen-independent_coproporphy; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00538; hemN; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Cytoplasm; Direct protein sequencing; Iron;
KW Iron-sulfur; Metal-binding; Oxidoreductase; Porphyrin biosynthesis;
KW Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..457
FT /note="Oxygen-independent coproporphyrinogen III oxidase"
FT /id="PRO_0000109941"
FT DOMAIN 47..280
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 56
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 62
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 66
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 68..70
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 69
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 112
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 113..114
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 145
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 172
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 184
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 209
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 243
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT BINDING 329
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:14633981,
FT ECO:0007744|PDB:1OLT"
FT MUTAGEN 56
FT /note="Y->A,L: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12114526,
FT ECO:0000269|PubMed:15967800"
FT MUTAGEN 56
FT /note="Y->F: Decreases activity by 50%."
FT /evidence="ECO:0000269|PubMed:12114526,
FT ECO:0000269|PubMed:15967800"
FT MUTAGEN 58
FT /note="H->L: Results in loss of iron-sulfur cluster and
FT activity."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 62
FT /note="C->S: Results in loss of iron-sulfur cluster and
FT activity."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 66
FT /note="C->S: Results in loss of iron-sulfur cluster and
FT activity."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 68
FT /note="F->L: No effect."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 69
FT /note="C->S: Results in loss of iron-sulfur cluster and
FT activity."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 71
FT /note="C->S: No effect on iron-sulfur cluster, but results
FT in activity loss."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 111
FT /note="G->V: Loss of activity and much less iron-sulfur
FT cluster formed; when associated with V-113."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 113
FT /note="G->V: Loss of activity and much less iron-sulfur
FT cluster formed; when associated with V-111."
FT /evidence="ECO:0000269|PubMed:12114526"
FT MUTAGEN 145
FT /note="E->A,I: Loss of activity. Iron content reduced by
FT about 80%."
FT /evidence="ECO:0000269|PubMed:15967800"
FT MUTAGEN 310
FT /note="F->A,L: Loss of activity. Iron content reduced by
FT about 50%. Can cleave up to one molecule of S-adenosyl-L-
FT methionine (in vitro)."
FT /evidence="ECO:0000269|PubMed:15967800"
FT MUTAGEN 311
FT /note="Q->A: Loss of activity. No change in iron content.
FT Can cleave up to one molecule of S-adenosyl-L-methionine
FT (in vitro)."
FT /evidence="ECO:0000269|PubMed:15967800"
FT MUTAGEN 329
FT /note="I->A: Loss of activity. No change in iron content.
FT Can cleave up to one molecule of S-adenosyl-L-methionine
FT (in vitro)."
FT /evidence="ECO:0000269|PubMed:15967800"
FT CONFLICT 232
FT /note="L -> V (in Ref. 2; CAA57578)"
FT /evidence="ECO:0000305"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 38..45
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 80..96
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 105..113
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 120..133
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 136..146
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 154..161
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 166..172
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 176..182
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 188..200
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 207..213
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 219..232
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 235..241
FT /evidence="ECO:0007829|PDB:1OLT"
FT TURN 246..248
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 250..254
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 263..279
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 283..286
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 296..303
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 313..315
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 329..332
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 343..353
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 357..362
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 365..380
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 381..384
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 385..391
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 396..399
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 401..412
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 415..418
FT /evidence="ECO:0007829|PDB:1OLT"
FT STRAND 420..425
FT /evidence="ECO:0007829|PDB:1OLT"
FT TURN 427..429
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 430..432
FT /evidence="ECO:0007829|PDB:1OLT"
FT HELIX 433..438
FT /evidence="ECO:0007829|PDB:1OLT"
SQ SEQUENCE 457 AA; 52729 MW; 047EBB65D9B8F133 CRC64;
MSVQQIDWDL ALIQKYNYSG PRYTSYPTAL EFSEDFGEQA FLQAVARYPE RPLSLYVHIP
FCHKLCYFCG CNKIVTRQQH KADQYLDALE QEIVHRAPLF AGRHVSQLHW GGGTPTYLNK
AQISRLMKLL RENFQFNADA EISIEVDPRE IELDVLDHLR AEGFNRLSMG VQDFNKEVQR
LVNREQDEEF IFALLNHARE IGFTSTNIDL IYGLPKQTPE SFAFTLKRVA ELNPDRLSVF
NYAHLPTIFA AQRKIKDADL PSPQQKLDIL QETIAFLTQS GYQFIGMDHF ARPDDELAVA
QREGVLHRNF QGYTTQGDTD LLGMGVSAIS MIGDCYAQNQ KELKQYYQQV DEQGNALWRG
IALTRDDCIR RDVIKSLICN FRLDYAPIEK QWDLHFADYF AEDLKLLAPL AKDGLVDVDE
KGIQVTAKGR LLIRNICMCF DTYLRQKARM QQFSRVI
