1C41

CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1c41a_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
B	d1c41b_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
C	d1c41c_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
D	d1c41d_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
E	d1c41e_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
F	d1c41f_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
G	d1c41g_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
H	d1c41h_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
I	d1c41i_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)
J	d1c41j_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	Lumazine synthase	Lumazine synthase	(Pyricularia grisea ) [TaxId: 148305 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Lumazine synthase	8031653	4003586	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Lumazine synthase	8044031	3001085	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Lumazine synthase	8044031	3001085	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	DMRL_synthase	e1c41A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
B	DMRL_synthase	e1c41B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
C	DMRL_synthase	e1c41C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
D	DMRL_synthase	e1c41D1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
E	DMRL_synthase	e1c41E1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
F	DMRL_synthase	e1c41F1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
G	DMRL_synthase	e1c41G1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
H	DMRL_synthase	e1c41H1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
I	DMRL_synthase	e1c41I1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
J	DMRL_synthase	e1c41J1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
B	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
C	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
D	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
E	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
F	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
G	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
H	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
I	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
J	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF00885	6,7-dimethyl-8-ribityllumazine synthase (DMRL_synthase)	6,7-dimethyl-8-ribityllumazine synthase	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function f ...	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	LUMAZINE SYNTHASE	6,7-dimethyl-8-ribityllumazine synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process water-soluble vitamin metabolic process riboflavin metabolic process	protein-containing complex catalytic complex riboflavin synthase complex transferase complex membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope protein-containing complex catalytic complex riboflavin synthase complex transferase complex membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope cellular anatomical structure organelle lumen organelle mitochondrial envelope cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR034964	Lumazine synthase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR002180	Lumazine/riboflavin synthase	Family

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.