Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae.
Coproporphyrinogen oxidase (CPO) is an essential enzyme that catalyzes the sixth step of the heme biosynthetic pathway. Unusually for heme biosynthetic enzymes, CPO exists in two evolutionarily and mechanistically distinct families, with eukaryotes and some prokaryotes employing members of the highly conserved oxygen-dependent CPO family. Here, we report the crystal structure of the oxygen-dependent CPO from Saccharomyces cerevisiae (Hem13p), which was determined by optimized sulfur anomalous scattering and refined to a resolution of 2.0 A. The protein adopts a novel structure that is quite different from predicted models and features a central flat seven-stranded anti-parallel sheet that is flanked by helices. The dimeric assembly, which is seen in different crystal forms, is formed by packing of helices and a short isolated strand that forms a beta-ladder with its counterpart in the partner subunit. The deep active-site cleft is lined by conserved residues and has been captured in open and closed conformations in two different crystal forms. A substratesized cavity is completely buried in the closed conformation by the approximately 8-A movement of a helix that forms a lid over the active site. The structure therefore suggests residues that likely play critical roles in catalysis and explains the deleterious effect of many of the mutations associated with the disease hereditary coproporphyria.
Phillips
John D
JD
Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.
Whitby
Frank G
FG
Warby
Christy A
CA
Labbe
Pierre
P
Yang
Cheng
C
Pflugrath
James W
JW
Ferrara
Joseph D
JD
Robinson
Howard
H
Kushner
James P
JP
Hill
Christopher P
CP
D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D003304:Coproporphyrinogen Oxidase / Q000737:chemistry* / Q000378:metabolism; D003305:Coproporphyrinogens / Q000737:chemistry; D018360:Crystallography, X-Ray; D018076:DNA, Complementary / Q000378:metabolism; D019281:Dimerization; D006418:Heme / Q000737:chemistry; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D011524:Protoporphyrins / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
D003305:Coproporphyrinogens; D018076:DNA, Complementary; D011524:Protoporphyrins; D029701:Saccharomyces cerevisiae Proteins; C028026:coproporphyrinogen III; D006418:Heme; C011539:protoporphyrinogen; D003304:Coproporphyrinogen Oxidase