1PJQ | pdb_00001pjq

Structure and function of CysG, the multifunctional methyltransferase/dehydrogenase/ferrochelatase for 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
Protein Modification Annotation
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	d1pjqa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Siroheme synthase N-terminal domain-like	Siroheme synthase CysG, domain 1	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d1pjqa2	Alpha and beta proteins (a/b)	Tetrapyrrole methylase	Tetrapyrrole methylase	Tetrapyrrole methylase	Siroheme synthase CysG, domains 4 and 5	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d1pjqa3	Multi-domain proteins (alpha and beta)	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase CysG, domains 2 and 3	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d1pjqb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Siroheme synthase N-terminal domain-like	Siroheme synthase CysG, domain 1	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d1pjqb2	Alpha and beta proteins (a/b)	Tetrapyrrole methylase	Tetrapyrrole methylase	Tetrapyrrole methylase	Siroheme synthase CysG, domains 4 and 5	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d1pjqb3	Multi-domain proteins (alpha and beta)	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase middle domains-like	Siroheme synthase CysG, domains 2 and 3	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tetrapyrrole methylase	8001041	3000017	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CysG/Met8-like	8057834	3000045	SCOP2B (2022-06-29)
B	SCOP2 Family	Siroheme synthase-like	8001039	4000066	SCOP2 (2022-06-29)
B	SCOP2 Family	Tetrapyrrole methylase	8001040	4000056	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CysG/Met8-like	8057834	3000045	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Tetrapyrrole methylase	8001041	3000017	SCOP2 (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		e1pjqA1	A: alpha-helical domain in siroheme synthase middle domains-like	X: alpha-helical domain in siroheme synthase middle domains-like	H: alpha-helical domain in siroheme synthase middle domains-like	T: CysG_dimeriser	F:	ECOD (20:10:01)
A		e1pjqA2	A: SSH domain in siroheme synthase middle domains-like	X: SSH domain in siroheme synthase middle domains-like	H: SSH domain in siroheme synthase middle domains-like	T: Sirohm_synth_M	F:	ECOD (20:10:01)
A		e1pjqA3	A: Rossmann-like	X: Rossmann-related	H: NAD(P)-binding Rossmann-fold domains	T: NAD_binding_7	F:	ECOD (20:10:01)
A		e1pjqA6	A: jelly-roll	X: AOC barrel-like	H: AOC barrel-like	T:	F:	ECOD (20:10:01)
B		e1pjqB2	A: SSH domain in siroheme synthase middle domains-like	X: SSH domain in siroheme synthase middle domains-like	H: SSH domain in siroheme synthase middle domains-like	T: Sirohm_synth_M	F:	ECOD (20:10:01)
B		e1pjqB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
B		e1pjqB4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
B		e1pjqB3	A: F-type ATP synthase subunit b	X: Bacterial cell wall synthesis membrane enzyme MraY-related	H: Bacterial cell wall synthesis membrane enzyme MraY-related	T: Phage_int_SAM_6	F:	ECOD (20:10:01)

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	1.10.8.210	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.1010.10	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
A	3.30.950.10	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	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	1.10.8.210	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.40.1010.10	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
B	3.30.950.10	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	PF00590	Tetrapyrrole (Corrin/Porphyrin) Methylases (TP_methylase)	Tetrapyrrole (Corrin/Porphyrin) Methylases	This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function, including Swiss:P45528. This family includes the methylase Dipthine synthase.	Domain
A, B	PF13241	Putative NAD(P)-binding (NAD_binding_7)	Putative NAD(P)-binding	This domain is found in fungi, plants, archaea and bacteria.	Domain
A, B	PF10414	Sirohaem synthase dimerisation region (CysG_dimeriser)	Sirohaem synthase dimerisation region	Bacterial sulfur metabolism depends on the iron-containing porphinoid sirohaem. CysG, S-adenosyl-L-methionine (SAM)-dependent bis-methyltransferase, dehydrogenase and ferrochelatase, synthesises sirohaem from uroporphyrinogen III via reactions which ...	Bacterial sulfur metabolism depends on the iron-containing porphinoid sirohaem. CysG, S-adenosyl-L-methionine (SAM)-dependent bis-methyltransferase, dehydrogenase and ferrochelatase, synthesises sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer of two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues in the CysG_dimeriser region to produce a series of active sites, accounting for CysG's multifunctionality, catalysing four diverse reactions: two SAM-dependent methylations, NAD+-dependent tetrapyrrole dehydrogenation and metal chelation. The CysG_dimeriser region holding the two protomers together is of 74 residues [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Siroheme synthase	sirohydrochlorin ferrochelatase activity lyase activity ferrochelatase activity catalytic 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 NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding sirohydrochlorin ferrochelatase activity lyase activity ferrochelatase activity catalytic 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 NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding C-methyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity uroporphyrin-III C-methyltransferase activity	heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process siroheme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process heme metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process heme biosynthetic process siroheme biosynthetic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process small molecule metabolic process methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035996	Tetrapyrrole methylase superfamily	Homologous Superfamily
A, B	IPR014776	Tetrapyrrole methylase, subdomain 2	Homologous Superfamily
A, B	IPR037115	Sirohaem synthase, dimerisation domain superfamily	Homologous Superfamily
A, B	IPR006366	Uroporphyrin-III C-methyltransferase	Domain
A, B	IPR014777	Tetrapyrrole methylase, subdomain 1	Homologous Superfamily
A, B	IPR012409	Sirohaem synthase	Family
A, B	IPR028281	Siroheme synthase, central domain	Domain
A, B	IPR019478	Sirohaem synthase, dimerisation domain	Domain
A, B	IPR003043	Uroporphiryn-III C-methyltransferase, conserved site	Conserved Site
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR000878	Tetrapyrrole methylase	Domain
A, B	IPR006367	Sirohaem synthase, N-terminal	Domain
A, B	IPR050161	Siroheme/cobalamin biosynthesis enzyme	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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

Chains	Enzyme Name	Description	Catalytic Residues
A	uroporphyrinogen-III C-methyltransferase M-CSA #702	The reference protein (CysG) covers three different domains/functions each component of which can be found as independent proteins in other organisms. This entry relates to the uroporphyrinogen-III C-methyltransferase function (residues 216-448 in the reference protein). This catalytic site catalyses two sequential methylation reactions using S-andenosyl-L-methionine (SAM), the first forming precorrin-1 and the second leading to the formation of precorrin-2. It is the first of three steps leading to the formation of siroheme from uroporphyrinogen III.	Defined by 3 residues: ASP:A-248LYS:A-270MET:A-382 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.107 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.107 EC: 1 (PDB Primary Data) Search M-CSA Motif + EC 1 EC: 4.99.1 (PDB Primary Data) Search M-CSA Motif + EC 4.99.1 EC: 4.99.1.4 (UniProt) Search M-CSA Motif + EC 4.99.1.4 EC: 1.3.1.76 (UniProt) Search M-CSA Motif + EC 1.3.1.76

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.