HEM6_YEAST
ID HEM6_YEAST Reviewed; 328 AA.
AC P11353; D6VS32;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=Oxygen-dependent coproporphyrinogen-III oxidase;
DE Short=COX;
DE Short=Coprogen oxidase;
DE Short=Coproporphyrinogenase;
DE EC=1.3.3.3 {ECO:0000269|PubMed:3516695};
GN Name=HEM13; OrderedLocusNames=YDR044W; ORFNames=YD5112.02;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2838478; DOI=10.1016/s0021-9258(19)81577-6;
RA Zagorec M., Buhler J.-M., Treich I., Keng T., Guarente L., Labbe-Bois R.;
RT "Isolation, sequence, and regulation by oxygen of the yeast HEM13 gene
RT coding for coproporphyrinogen oxidase.";
RL J. Biol. Chem. 263:9718-9724(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP PROTEIN SEQUENCE OF 2-10, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBCELLULAR LOCATION, AND SUBUNIT.
RX PubMed=3516695; DOI=10.1111/j.1432-1033.1986.tb09617.x;
RA Camadro J.-M., Chambon H., Jolles J., Labbe P.;
RT "Purification and properties of coproporphyrinogen oxidase from the yeast
RT Saccharomyces cerevisiae.";
RL Eur. J. Biochem. 156:579-587(1986).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), SUBUNIT, AND DISULFIDE BOND.
RX PubMed=15194705; DOI=10.1074/jbc.m406050200;
RA Phillips J.D., Whitby F.G., Warby C.A., Labbe P., Yang C., Pflugrath J.W.,
RA Ferrara J.D., Robinson H., Kushner J.P., Hill C.P.;
RT "Crystal structure of the oxygen-dependant coproporphyrinogen oxidase
RT (Hem13p) of Saccharomyces cerevisiae.";
RL J. Biol. Chem. 279:38960-38968(2004).
CC -!- FUNCTION: Involved in the heme biosynthesis. Catalyzes the aerobic
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:0000269|PubMed:3516695}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=coproporphyrinogen III + 2 H(+) + O2 = 2 CO2 + 2 H2O +
CC protoporphyrinogen IX; Xref=Rhea:RHEA:18257, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57307, ChEBI:CHEBI:57309; EC=1.3.3.3;
CC Evidence={ECO:0000269|PubMed:3516695};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18258;
CC Evidence={ECO:0000269|PubMed:3516695};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.05 uM for coproporphyrinogen {ECO:0000269|PubMed:3516695};
CC pH dependence:
CC Optimum pH is 7.6. {ECO:0000269|PubMed:3516695};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2
CC route): step 1/1. {ECO:0000305|PubMed:3516695}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15194705,
CC ECO:0000269|PubMed:3516695}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:3516695}.
CC -!- MISCELLANEOUS: Present with 22000 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the aerobic coproporphyrinogen-III oxidase
CC family. {ECO:0000305}.
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DR EMBL; J03873; AAA34529.1; -; Genomic_DNA.
DR EMBL; Z49812; CAA89966.1; -; Genomic_DNA.
DR EMBL; AY557656; AAS55982.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11892.1; -; Genomic_DNA.
DR PIR; S55079; DEBYCH.
DR RefSeq; NP_010329.1; NM_001180352.1.
DR PDB; 1TK1; X-ray; 1.90 A; A=6-265.
DR PDB; 1TKL; X-ray; 2.00 A; A/B=3-328.
DR PDB; 1TLB; X-ray; 2.40 A; A/D/Q/S/U/W=3-328.
DR PDB; 1TXN; X-ray; 1.70 A; A/B=1-328.
DR PDBsum; 1TK1; -.
DR PDBsum; 1TKL; -.
DR PDBsum; 1TLB; -.
DR PDBsum; 1TXN; -.
DR AlphaFoldDB; P11353; -.
DR SMR; P11353; -.
DR BioGRID; 32099; 230.
DR DIP; DIP-1614N; -.
DR IntAct; P11353; 10.
DR MINT; P11353; -.
DR STRING; 4932.YDR044W; -.
DR iPTMnet; P11353; -.
DR MaxQB; P11353; -.
DR PaxDb; P11353; -.
DR PRIDE; P11353; -.
DR EnsemblFungi; YDR044W_mRNA; YDR044W; YDR044W.
DR GeneID; 851614; -.
DR KEGG; sce:YDR044W; -.
DR SGD; S000002451; HEM13.
DR VEuPathDB; FungiDB:YDR044W; -.
DR eggNOG; KOG1518; Eukaryota.
DR GeneTree; ENSGT00390000017311; -.
DR HOGENOM; CLU_026169_0_0_1; -.
DR InParanoid; P11353; -.
DR OMA; HDKGTLF; -.
DR BioCyc; YEAST:YDR044W-MON; -.
DR BRENDA; 1.3.3.3; 984.
DR Reactome; R-SCE-189451; Heme biosynthesis.
DR UniPathway; UPA00251; UER00322.
DR EvolutionaryTrace; P11353; -.
DR PRO; PR:P11353; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P11353; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IBA:GO_Central.
DR GO; GO:0004109; F:coproporphyrinogen oxidase activity; IDA:SGD.
DR GO; GO:0042803; F:protein homodimerization activity; ISS:UniProtKB.
DR GO; GO:0006783; P:heme biosynthetic process; IMP:SGD.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.1500.10; -; 1.
DR InterPro; IPR001260; Coprogen_oxidase_aer.
DR InterPro; IPR036406; Coprogen_oxidase_aer_sf.
DR InterPro; IPR018375; Coprogen_oxidase_CS.
DR PANTHER; PTHR10755; PTHR10755; 1.
DR Pfam; PF01218; Coprogen_oxidas; 1.
DR PIRSF; PIRSF000166; Coproporphyri_ox; 1.
DR PRINTS; PR00073; COPRGNOXDASE.
DR SUPFAM; SSF102886; SSF102886; 1.
DR PROSITE; PS01021; COPROGEN_OXIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Disulfide bond;
KW Heme biosynthesis; Oxidoreductase; Porphyrin biosynthesis;
KW Reference proteome.
FT CHAIN 1..328
FT /note="Oxygen-dependent coproporphyrinogen-III oxidase"
FT /id="PRO_0000109878"
FT REGION 57..66
FT /note="Important for dimerization"
FT /evidence="ECO:0000250"
FT REGION 266..302
FT /note="Important for dimerization"
FT /evidence="ECO:0000250"
FT ACT_SITE 131
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 117
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 133..135
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 285..290
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 201
FT /note="Important for dimerization"
FT /evidence="ECO:0000250"
FT DISULFID 193
FT /note="Interchain"
FT /evidence="ECO:0000269|PubMed:15194705"
FT CONFLICT 226
FT /note="K -> N (in Ref. 1; AAA34529)"
FT /evidence="ECO:0000305"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:1TKL"
FT HELIX 12..32
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:1TKL"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:1TKL"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 62..78
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 80..84
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:1TKL"
FT STRAND 109..124
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 129..140
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 144..158
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 164..179
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 185..189
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 193..200
FT /evidence="ECO:0007829|PDB:1TXN"
FT STRAND 204..207
FT /evidence="ECO:0007829|PDB:1TKL"
FT STRAND 209..216
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 221..232
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 235..244
FT /evidence="ECO:0007829|PDB:1TXN"
FT TURN 245..248
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 253..263
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 265..269
FT /evidence="ECO:0007829|PDB:1TXN"
FT HELIX 275..282
FT /evidence="ECO:0007829|PDB:1TKL"
FT HELIX 288..291
FT /evidence="ECO:0007829|PDB:1TKL"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:1TKL"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:1TKL"
FT HELIX 312..321
FT /evidence="ECO:0007829|PDB:1TKL"
SQ SEQUENCE 328 AA; 37712 MW; 9C166F03BD0B0B4C CRC64;
MPAPQDPRNL PIRQQMEALI RRKQAEITQG LESIDTVKFH ADTWTRGNDG GGGTSMVIQD
GTTFEKGGVN VSVVYGQLSP AAVSAMKADH KNLRLPEDPK TGLPVTDGVK FFACGLSMVI
HPVNPHAPTT HLNYRYFETW NQDGTPQTWW FGGGADLTPS YLYEEDGQLF HQLHKDALDK
HDTALYPRFK KWCDEYFYIT HRKETRGIGG IFFDDYDERD PQEILKMVED CFDAFLPSYL
TIVKRRKDMP YTKEEQQWQA IRRGRYVEFN LIYDRGTQFG LRTPGSRVES ILMSLPEHAS
WLYNHHPAPG SREAKLLEVT TKPREWVK
