P11353 (HEM6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Coproporphyrinogen-III oxidase
Short name=COX
Short name=Coprogen oxidase
Short name=Coproporphyrinogenase
EC=1.3.3.3

Gene names

Name:	HEM13
Ordered Locus Names:	YDR044W
ORF Names:	YD5112.02

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	328 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Key enzyme in heme biosynthesis. Catalyzes the oxidative decarboxylation of propionic acid side chains of rings A and B of coproporphyrinogen III By similarity.
Catalytic activity	Coproporphyrinogen-III + O2 + 2 H+ = protoporphyrinogen-IX + 2 CO2 + 2 H2O.
Pathway	Porphyrin metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (O2 route): step 1/1.
Subunit structure	Homodimer. Ref.8
Subcellular location	Cytoplasm Ref.6.
Miscellaneous	Present with 22000 molecules/cell in log phase SD medium. Ref.7
Sequence similarities	Belongs to the aerobic coproporphyrinogen-III oxidase family.

Ontologies

Keywords
Biological process	Heme biosynthesis Porphyrin biosynthesis
Cellular component	Cytoplasm
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	heme biosynthetic process Inferred from mutant phenotype. Source: SGD
Cellular component	cytosol Inferred from direct assay Ref.5. Source: SGD
Molecular function	coproporphyrinogen oxidase activity Inferred from direct assay Ref.5. Source: SGD protein homodimerization activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ESS1	P22696	1	EBI-8257,EBI-6679
PRP40	P33203	1	EBI-8257,EBI-701
SET2	P46995	1	EBI-8257,EBI-16985
YFL010C	P43582	1	EBI-8257,EBI-22766

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 328

328

Coproporphyrinogen-III oxidase

PRO_0000109878

Regions

Region

57 – 66

10

Important for dimerization By similarity

Region

133 – 135

3

Substrate binding By similarity

Region

266 – 302

37

Important for dimerization By similarity

Region

285 – 290

6

Substrate binding By similarity

Sites

Active site

131

1

Proton donor By similarity

Binding site

117

1

Substrate By similarity

Site

201

1

Important for dimerization By similarity

Amino acid modifications

Disulfide bond

193

Interchain Ref.8

Experimental info

Sequence conflict

226

1

K → N in AAA34529. Ref.1

Secondary structure

1

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328

Helix Strand Turn

Details...

Helix

12 – 32

21

Beta strand

35 – 37

3

Beta strand

54 – 60

7

Beta strand

62 – 78

17

Helix

80 – 86

7

Helix

87 – 89

3

Beta strand

109 – 124

16

Beta strand

129 – 139

11

Beta strand

149 – 158

10

Helix

164 – 179

16

Helix

185 – 189

5

Beta strand

209 – 216

8

Helix

221 – 246

26

Helix

253 – 263

11

Helix

266 – 272

7

Helix

275 – 282

8

Helix

288 – 291

4

Helix

292 – 294

3

Beta strand

297 – 300

4

Helix

312 – 321

10

Sequences

	Sequence		Length	Mass (Da)
	P11353 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: 9C166F03BD0B0B4C	FASTA	328	37,712
	10 20 30 40 50 60 MPAPQDPRNL PIRQQMEALI RRKQAEITQG LESIDTVKFH ADTWTRGNDG GGGTSMVIQD 70 80 90 100 110 120 GTTFEKGGVN VSVVYGQLSP AAVSAMKADH KNLRLPEDPK TGLPVTDGVK FFACGLSMVI 130 140 150 160 170 180 HPVNPHAPTT HLNYRYFETW NQDGTPQTWW FGGGADLTPS YLYEEDGQLF HQLHKDALDK 190 200 210 220 230 240 HDTALYPRFK KWCDEYFYIT HRKETRGIGG IFFDDYDERD PQEILKMVED CFDAFLPSYL 250 260 270 280 290 300 TIVKRRKDMP YTKEEQQWQA IRRGRYVEFN LIYDRGTQFG LRTPGSRVES ILMSLPEHAS 310 320 WLYNHHPAPG SREAKLLEVT TKPREWVK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation, sequence, and regulation by oxygen of the yeast HEM13 gene coding for coproporphyrinogen oxidase." Zagorec M., Buhler J.-M., Treich I., Keng T., Guarente L., Labbe-Bois R. J. Biol. Chem. 263:9718-9724(1988) [PubMed: 2838478] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Purification and properties of coproporphyrinogen oxidase from the yeast Saccharomyces cerevisiae." Camadro J.-M., Chambon H., Jolles J., Labbe P. Eur. J. Biochem. 156:579-587(1986) [PubMed: 3516695] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
[6]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae." Phillips J.D., Whitby F.G., Warby C.A., Labbe P., Yang C., Pflugrath J.W., Ferrara J.D., Robinson H., Kushner J.P., Hill C.P. J. Biol. Chem. 279:38960-38968(2004) [PubMed: 15194705] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), SUBUNIT, DISULFIDE BOND.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J03873 Genomic DNA. Translation: AAA34529.1.
Z49812 Genomic DNA. Translation: CAA89966.1.
AY557656 Genomic DNA. Translation: AAS55982.1.
BK006938 Genomic DNA. Translation: DAA11892.1.

PIR

DEBYCH. S55079.

RefSeq

NP_010329.1. NM_001180352.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1TK1	X-ray	1.90	A	6-265	[»]
1TKL	X-ray	2.00	A/B	3-328	[»]
1TLB	X-ray	2.40	A/D/Q/S/U/W	3-328	[»]
1TXN	X-ray	1.70	A/B	1-328	[»]

ProteinModelPortal

P11353.

SMR

P11353. Positions 3-328.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1614N.

IntAct

P11353. 10 interactions.

MINT

MINT-403879.

STRING

P11353.

Proteomic databases

PeptideAtlas

P11353.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR044W; YDR044W; YDR044W.

GeneID

851614.

KEGG

sce:YDR044W.

NMPDR

fig|4932.3.peg.1074.

Organism-specific databases

CYGD

YDR044w.

SGD

S000002451. HEM13.

Phylogenomic databases

eggNOG

fuNOG05187.

GeneTree

EFGT00050000004574.

HOGENOM

HBG631180.

OMA

VFKPWCD.

OrthoDB

EOG4DNJD1.

Gene expression databases

ArrayExpress

P11353.

Genevestigator

P11353.

GermOnline

YDR044W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001260. Coprogen_oxidase_aer.
IPR018375. Coprogen_oxidase_CS.
[Graphical view]

Gene3D

G3DSA:3.40.1500.10. Coprogen_oxidas. 1 hit.

KO

K00228.

PANTHER

PTHR10755. Coprogen_oxidas. 1 hit.

Pfam

PF01218. Coprogen_oxidas. 1 hit.
[Graphical view]

PIRSF

PIRSF000166. Coproporphyri_ox. 1 hit.

PRINTS

PR00073. COPRGNOXDASE.

SUPFAM

SSF102886. Coprogen_oxidas. 1 hit.

PROSITE

PS01021. COPROGEN_OXIDASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

969136.

Entry information

Entry name

HEM6_YEAST

Accession

Primary (citable) accession number: P11353
Secondary accession number(s): D6VS32

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	October 1, 1996
Last modified:	December 14, 2011
This is version 121 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program