4J07

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

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	d4j07a_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	automated matches	automated matches	(Mycobacterium leprae Br4923 ) [TaxId: 561304 ],	SCOPe (2.08)
B	d4j07b_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	automated matches	automated matches	(Mycobacterium leprae Br4923 ) [TaxId: 561304 ],	SCOPe (2.08)
C	d4j07c_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	automated matches	automated matches	(Mycobacterium leprae Br4923 ) [TaxId: 561304 ],	SCOPe (2.08)
D	d4j07d_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	automated matches	automated matches	(Mycobacterium leprae Br4923 ) [TaxId: 561304 ],	SCOPe (2.08)
E	d4j07e_	Alpha and beta proteins (a/b)	Lumazine synthase	Lumazine synthase	automated matches	automated matches	(Mycobacterium leprae Br4923 ) [TaxId: 561304 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lumazine synthase	8066579	3001085	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lumazine synthase	8066579	3001085	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lumazine synthase	8066579	3001085	SCOP2B (2022-06-29)
D	SCOP2 Family	Lumazine synthase	8066578	4003586	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Lumazine synthase	8066579	3001085	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Lumazine synthase	8066579	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	e4j07A1	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	e4j07B2	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	e4j07C2	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	e4j07D2	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	e4j07E2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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	6,7-dimethyl-8-ribityllumazine 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 cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process small molecule metabolic process cellular process water-soluble vitamin metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process small molecule metabolic process cellular process water-soluble vitamin metabolic process riboflavin metabolic process	protein-containing complex catalytic complex riboflavin synthase complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
A, B, C, D, E	IPR034964	Lumazine synthase	Family
A, B, C, D, E	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.