1KYQ

Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1kyqa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Siroheme synthase N-terminal domain-like	Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1kyqa2	Multi-domain proteins (alpha and beta)	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1kyqb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Siroheme synthase N-terminal domain-like	Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1kyqb2	Multi-domain proteins (alpha and beta)	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1kyqc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Siroheme synthase N-terminal domain-like	Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1kyqc2	Multi-domain proteins (alpha and beta)	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CysG/Met8-like	8001034	3000045	SCOP2B (2022-06-29)
B	SCOP2 Family	Siroheme synthase-like	8001033	4000066	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CysG/Met8-like	8001034	3000045	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	CysG/Met8-like	8001034	3000045	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Sirohm_synth_C	e1kyqA1	A: alpha superhelices	X: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	H: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	T: alpha-helical domain in siroheme synthase middle domains-like	F: Sirohm_synth_C	ECOD (1.6)
A	Sirohm_synth_M	e1kyqA2	A: a+b duplicates or obligate multimers	X: SSH domain in siroheme synthase middle domains-like (From Topology)	H: SSH domain in siroheme synthase middle domains-like (From Topology)	T: SSH domain in siroheme synthase middle domains-like	F: Sirohm_synth_M	ECOD (1.6)
A	NAD_binding_7	e1kyqA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_7	ECOD (1.6)
B	Sirohm_synth_C	e1kyqB1	A: alpha superhelices	X: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	H: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	T: alpha-helical domain in siroheme synthase middle domains-like	F: Sirohm_synth_C	ECOD (1.6)
B	Sirohm_synth_M	e1kyqB2	A: a+b duplicates or obligate multimers	X: SSH domain in siroheme synthase middle domains-like (From Topology)	H: SSH domain in siroheme synthase middle domains-like (From Topology)	T: SSH domain in siroheme synthase middle domains-like	F: Sirohm_synth_M	ECOD (1.6)
B	NAD_binding_7	e1kyqB4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_7	ECOD (1.6)
C	Sirohm_synth_C	e1kyqC1	A: alpha superhelices	X: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	H: alpha-helical domain in siroheme synthase middle domains-like (From Topology)	T: alpha-helical domain in siroheme synthase middle domains-like	F: Sirohm_synth_C	ECOD (1.6)
C	Sirohm_synth_M	e1kyqC4	A: a+b duplicates or obligate multimers	X: SSH domain in siroheme synthase middle domains-like (From Topology)	H: SSH domain in siroheme synthase middle domains-like (From Topology)	T: SSH domain in siroheme synthase middle domains-like	F: Sirohm_synth_M	ECOD (1.6)
C	NAD_binding_7	e1kyqC3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_7	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	CATH (4.3.0)
A	1.10.3280.10	Mainly Alpha	Orthogonal Bundle	Siro heme synthase C-terminal domain-like	Siroheme synthase	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	CATH (4.3.0)
B	1.10.3280.10	Mainly Alpha	Orthogonal Bundle	Siro heme synthase C-terminal domain-like	Siroheme synthase	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.30.160.110	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Sirohaem synthase, central domain	CATH (4.3.0)
C	1.10.3280.10	Mainly Alpha	Orthogonal Bundle	Siro heme synthase C-terminal domain-like	Siroheme synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF14823	Sirohaem biosynthesis protein C-terminal (Sirohm_synth_C)	Sirohaem biosynthesis protein C-terminal	This domain is the C-terminus of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are loca ...	This domain is the C-terminus of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, Pfam:PF13241 [1].	Domain
A, B, C	PF14824	Sirohaem biosynthesis protein central (Sirohm_synth_M)	Sirohaem biosynthesis protein central	This is the central domain of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located ...	This is the central domain of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, Pfam:PF13241 [1].	Domain
A, B, C	PF13241	Putative NAD(P)-binding (NAD_binding_7)	Putative NAD(P)-binding	This domain is found in fungi, plants, archaea and bacteria.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Siroheme biosynthesis protein MET8	lyase activity ferrochelatase activity catalytic activity sirohydrochlorin ferrochelatase activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor precorrin-2 dehydrogenase activity oxidoreductase activity, acting on the CH-CH group of donors	heme metabolic process pigment metabolic process organonitrogen compound metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process organonitrogen compound biosynthetic process siroheme biosynthetic process pigment biosynthetic process organic cyclic compound metabolic process organic substance metabolic process tetrapyrrole biosynthetic process biosynthetic process siroheme metabolic process organic cyclic compound biosynthetic process heme metabolic process pigment metabolic process organonitrogen compound metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process organonitrogen compound biosynthetic process siroheme biosynthetic process pigment biosynthetic process organic cyclic compound metabolic process organic substance metabolic process tetrapyrrole biosynthetic process biosynthetic process siroheme metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process porphyrin-containing compound metabolic process sulfate assimilation cellular metabolic process sulfur compound metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR028281	Siroheme synthase, central domain	Domain
A, B, C	IPR028161	Siroheme biosynthesis protein Met8-like	Family
A, B, C	IPR028162	Siroheme biosynthesis protein Met8, C-terminal	Domain
A, B, C	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	precorrin-2 dehydrogenase M-CSA #610	Biosynthesis of the sirohaem cofactor is completed by Met8p, by a beta-NAD+-dependent dehydrogenation of precorrin-2 to produce sirohydrochlorin, followed by ferrochelation to generate sirohaem. Met8p has a similar role in cobalamin biosynthesis.	Defined by 1 residue: ASP:A-141 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 1 (PDB Primary Data) EC: 4.99.1.1 (PDB Primary Data)

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.