9G3P | pdb_00009g3p

Circularly permuted lumazine synthase 12-pentamer spherical cage

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
ZA	Beta-Casp	e9g3pZA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
Z	Beta-Casp	e9g3pZ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
YA	Beta-Casp	e9g3pYA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
Y	Beta-Casp	e9g3pY1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
XA	Beta-Casp	e9g3pXA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
X	Beta-Casp	e9g3pX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
WA	Beta-Casp	e9g3pWA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
W	Beta-Casp	e9g3pW1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
VA	Beta-Casp	e9g3pVA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
V	Beta-Casp	e9g3pV1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
UA	Beta-Casp	e9g3pUA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
U	Beta-Casp	e9g3pU1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
TA	Beta-Casp	e9g3pTA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
T	Beta-Casp	e9g3pT1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
SA	Beta-Casp	e9g3pSA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
S	Beta-Casp	e9g3pS1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
RA	Beta-Casp	e9g3pRA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
R	Beta-Casp	e9g3pR1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
QA	Beta-Casp	e9g3pQA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
Q	Beta-Casp	e9g3pQ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
PA	Beta-Casp	e9g3pPA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
P	Beta-Casp	e9g3pP1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
OA	Beta-Casp	e9g3pOA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
O	Beta-Casp	e9g3pO1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
NA	Beta-Casp	e9g3pNA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
N	Beta-Casp	e9g3pN1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
MA	Beta-Casp	e9g3pMA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
M	Beta-Casp	e9g3pM1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
LA	Beta-Casp	e9g3pLA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
L	Beta-Casp	e9g3pL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
KA	Beta-Casp	e9g3pKA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
K	Beta-Casp	e9g3pK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
JA	Beta-Casp	e9g3pJA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
J	Beta-Casp	e9g3pJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
IA	Beta-Casp	e9g3pIA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
I	Beta-Casp	e9g3pI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
HB	Beta-Casp	e9g3pHB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
HA	Beta-Casp	e9g3pHA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
H	Beta-Casp	e9g3pH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
GB	Beta-Casp	e9g3pGB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
GA	Beta-Casp	e9g3pGA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
G	Beta-Casp	e9g3pG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
FB	Beta-Casp	e9g3pFB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
FA	Beta-Casp	e9g3pFA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
F	Beta-Casp	e9g3pF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
EB	Beta-Casp	e9g3pEB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
EA	Beta-Casp	e9g3pEA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
E	Beta-Casp	e9g3pE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
DB	Beta-Casp	e9g3pDB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
DA	Beta-Casp	e9g3pDA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
D	Beta-Casp	e9g3pD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
CB	Beta-Casp	e9g3pCB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
CA	Beta-Casp	e9g3pCA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
C	Beta-Casp	e9g3pC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
BB	Beta-Casp	e9g3pBB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
BA	Beta-Casp	e9g3pBA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
B	Beta-Casp	e9g3pB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
AB	Beta-Casp	e9g3pAB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
AA	Beta-Casp	e9g3pAA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
A		e9g3pA01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F:	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, AA, AB, B, BA A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	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, AA, AB, B, BA A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	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 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 riboflavin metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex riboflavin synthase complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA, AB, B, BA A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
A, AA, AB, B, BA A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	IPR034964	Lumazine synthase	Family
A, AA, AB, B, BA A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	IPR002180	Lumazine/riboflavin synthase	Family

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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.