4G3M | pdb_00004g3m

Complex Structure of Bacillus subtilis RibG: The Deamination Process in Riboflavin Biosynthesis


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad4g3ma2 Alpha and beta proteins (a/b) Dihydrofolate reductase-like Dihydrofolate reductase-like RibD C-terminal domain-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Ad4g3ma1 Alpha and beta proteins (a/b) Cytidine deaminase-like Cytidine deaminase-like Deoxycytidylate deaminase-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Ad4g3ma3 Artifacts Tags Tags Tags N-terminal Tags (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Bd4g3mb2 Alpha and beta proteins (a/b) Dihydrofolate reductase-like Dihydrofolate reductase-like RibD C-terminal domain-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Bd4g3mb1 Alpha and beta proteins (a/b) Cytidine deaminase-like Cytidine deaminase-like Deoxycytidylate deaminase-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Bd4g3mb3 Artifacts Tags Tags Tags N-terminal Tags (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Cd4g3mc2 Alpha and beta proteins (a/b) Dihydrofolate reductase-like Dihydrofolate reductase-like RibD C-terminal domain-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Cd4g3mc1 Alpha and beta proteins (a/b) Cytidine deaminase-like Cytidine deaminase-like Deoxycytidylate deaminase-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Cd4g3mc3 Artifacts Tags Tags Tags N-terminal Tags (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Dd4g3md2 Alpha and beta proteins (a/b) Dihydrofolate reductase-like Dihydrofolate reductase-like RibD C-terminal domain-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Dd4g3md1 Alpha and beta proteins (a/b) Cytidine deaminase-like Cytidine deaminase-like Deoxycytidylate deaminase-like Riboflavin biosynthesis protein RibD (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)
Dd4g3md3 Artifacts Tags Tags Tags N-terminal Tags (Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCytidine deaminase-like 8037607 3001838 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyDihydrofolate reductase-like 8037605 3001255 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCytidine deaminase-like 8037607 3001838 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyDihydrofolate reductase-like 8037605 3001255 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyDihydrofolate reductase-like 8037605 3001255 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCytidine deaminase-like 8037607 3001838 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCytidine deaminase-like 8037607 3001838 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyDihydrofolate reductase-like 8037605 3001255 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AdCMP_cyt_deam_1e4g3mA4 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: dCMP_cyt_deam_1ECOD (1.6)
ARibD_Ce4g3mA3 A: a/b three-layered sandwichesX: Dihydrofolate reductases (From Topology)H: Dihydrofolate reductases (From Topology)T: Dihydrofolate reductasesF: RibD_CECOD (1.6)
BdCMP_cyt_deam_1e4g3mB4 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: dCMP_cyt_deam_1ECOD (1.6)
BRibD_Ce4g3mB3 A: a/b three-layered sandwichesX: Dihydrofolate reductases (From Topology)H: Dihydrofolate reductases (From Topology)T: Dihydrofolate reductasesF: RibD_CECOD (1.6)
CdCMP_cyt_deam_1e4g3mC4 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: dCMP_cyt_deam_1ECOD (1.6)
CRibD_Ce4g3mC3 A: a/b three-layered sandwichesX: Dihydrofolate reductases (From Topology)H: Dihydrofolate reductases (From Topology)T: Dihydrofolate reductasesF: RibD_CECOD (1.6)
DdCMP_cyt_deam_1e4g3mD4 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: dCMP_cyt_deam_1ECOD (1.6)
DRibD_Ce4g3mD3 A: a/b three-layered sandwichesX: Dihydrofolate reductases (From Topology)H: Dihydrofolate reductases (From Topology)T: Dihydrofolate reductasesF: RibD_CECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF00383Cytidine and deoxycytidylate deaminase zinc-binding region (dCMP_cyt_deam_1)Cytidine and deoxycytidylate deaminase zinc-binding regionDomain
A, B, C, D
PF01872RibD C-terminal domain (RibD_C)RibD C-terminal domainThe function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial ...The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial proteins Swiss:P95872. This family appears to be related to Pfam:PF00186.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D
Riboflavin biosynthesis protein RibD -