9RYM | pdb_00009rym

Aquifex aeolicus lumazine synthase 10-pentamer cage in complex with riboflavin synthase trimer

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
AA [auth E4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
BA [auth E5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
D [auth A1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
DA [auth F2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
E [auth A2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
EA [auth F3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
F [auth A3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
G [auth A4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
GA [auth F5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
H [auth A5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
HA [auth G1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
J [auth B2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
JA [auth G3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
K [auth B3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
KA [auth G4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
L [auth B4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
M [auth B5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
N [auth C1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
O [auth C2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
P [auth C3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
PA [auth H4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
Q [auth C4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
QA [auth H5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
R [auth C5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
RA [auth I1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
S [auth D1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
SA [auth I2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
T [auth D2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
TA [auth I3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
UA [auth I4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
V [auth D4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
VA [auth I5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
W [auth D5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
XA [auth J2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
Y [auth E2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
ZA [auth J4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
Z [auth E3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
YA [auth J3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
X [auth E1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
WA [auth J1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
U [auth D3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
OA [auth H3]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
NA [auth H2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
MA [auth H1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
LA [auth G5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
IA [auth G2]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
I [auth B1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
FA [auth F4]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
CA [auth F1]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)
AB [auth J5]	SCOP2B Superfamily	Lumazine synthase	8036909	3001085	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], DA [auth F2], E [auth A2], EA [auth F3], F [auth A3], FA [auth F4], G [auth A4], GA [auth F5], H [auth A5], HA [auth G1], I [auth B1], IA [auth G2], J [auth B2], JA [auth G3], K [auth B3], KA [auth G4], L [auth B4], LA [auth G5], M [auth B5], MA [auth H1], N [auth C1], NA [auth H2], O [auth C2], OA [auth H3], P [auth C3], PA [auth H4], Q [auth C4], QA [auth H5], R [auth C5], RA [auth I1], S [auth D1], SA [auth I2], T [auth D2], TA [auth I3], U [auth D3], UA [auth I4], V [auth D4], VA [auth I5], W [auth D5], WA [auth J1], X [auth E1], XA [auth J2], Y [auth E2], YA [auth J3], Z [auth E3], ZA [auth J4]	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
A [auth 1], B [auth 2], C [auth 3]	PF00677	Lumazine binding domain (Lum_binding)	Lumazine binding domain	This domain binds to derivatives of lumazine in some proteins. Some proteins have lost the residues involved in binding lumazine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], DA [auth F2], E [auth A2], EA [auth F3], F [auth A3], FA [auth F4], G [auth A4], GA [auth F5], H [auth A5], HA [auth G1], I [auth B1], IA [auth G2], J [auth B2], JA [auth G3], K [auth B3], KA [auth G4], L [auth B4], LA [auth G5], M [auth B5], MA [auth H1], N [auth C1], NA [auth H2], O [auth C2], OA [auth H3], P [auth C3], PA [auth H4], Q [auth C4], QA [auth H5], R [auth C5], RA [auth I1], S [auth D1], SA [auth I2], T [auth D2], TA [auth I3], U [auth D3], UA [auth I4], V [auth D4], VA [auth I5], W [auth D5], WA [auth J1], X [auth E1], XA [auth J2], Y [auth E2], YA [auth J3], Z [auth E3], ZA [auth J4]	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
A [auth 1], B [auth 2], C [auth 3]	Riboflavin synthase	riboflavin 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], DA [auth F2], E [auth A2], EA [auth F3], F [auth A3], FA [auth F4], G [auth A4], GA [auth F5], H [auth A5], HA [auth G1], I [auth B1], IA [auth G2], J [auth B2], JA [auth G3], K [auth B3], KA [auth G4], L [auth B4], LA [auth G5], M [auth B5], MA [auth H1], N [auth C1], NA [auth H2], O [auth C2], OA [auth H3], P [auth C3], PA [auth H4], Q [auth C4], QA [auth H5], R [auth C5], RA [auth I1], S [auth D1], SA [auth I2], T [auth D2], TA [auth I3], U [auth D3], UA [auth I4], V [auth D4], VA [auth I5], W [auth D5], WA [auth J1], X [auth E1], XA [auth J2], Y [auth E2], YA [auth J3], Z [auth E3], ZA [auth J4]	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], DA [auth F2], E [auth A2], EA [auth F3], F [auth A3], FA [auth F4], G [auth A4], GA [auth F5], H [auth A5], HA [auth G1], I [auth B1], IA [auth G2], J [auth B2], JA [auth G3], K [auth B3], KA [auth G4], L [auth B4], LA [auth G5], M [auth B5], MA [auth H1], N [auth C1], NA [auth H2], O [auth C2], OA [auth H3], P [auth C3], PA [auth H4], Q [auth C4], QA [auth H5], R [auth C5], RA [auth I1], S [auth D1], SA [auth I2], T [auth D2], TA [auth I3], U [auth D3], UA [auth I4], V [auth D4], VA [auth I5], W [auth D5], WA [auth J1], X [auth E1], XA [auth J2], Y [auth E2], YA [auth J3], Z [auth E3], ZA [auth J4]	IPR034964	Lumazine synthase	Family
AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], AA [auth E4], AB [auth J5], BA [auth E5], CA [auth F1], D [auth A1], DA [auth F2], E [auth A2], EA [auth F3], F [auth A3], FA [auth F4], G [auth A4], GA [auth F5], H [auth A5], HA [auth G1], I [auth B1], IA [auth G2], J [auth B2], JA [auth G3], K [auth B3], KA [auth G4], L [auth B4], LA [auth G5], M [auth B5], MA [auth H1], N [auth C1], NA [auth H2], O [auth C2], OA [auth H3], P [auth C3], PA [auth H4], Q [auth C4], QA [auth H5], R [auth C5], RA [auth I1], S [auth D1], SA [auth I2], T [auth D2], TA [auth I3], U [auth D3], UA [auth I4], V [auth D4], VA [auth I5], W [auth D5], WA [auth J1], X [auth E1], XA [auth J2], Y [auth E2], YA [auth J3], Z [auth E3], ZA [auth J4]	IPR002180	Lumazine/riboflavin synthase	Family
A [auth 1], B [auth 2], C [auth 3]	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
A [auth 1], B [auth 2], C [auth 3]	IPR026017	Lumazine-binding domain	Domain
A [auth 1], B [auth 2], C [auth 3]	IPR001783	Lumazine-binding protein	Family
A [auth 1], B [auth 2], C [auth 3]	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily

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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.