3AD8 | pdb_00003ad8

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
DSCOP2B SuperfamilySarcosine oxidase delta subunit-like 8090855 3002464 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyFolate-binding domain-like 8090858 3000025 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyFlavoreductase-like 8091767 3000055 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyBfd-like 8091773 3002540 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyFolate-binding domain-like 8091775 3000025 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyAminomethyltransferase beta-barrel domain-like 8091776 3000024 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyThioredoxin reductase-like 8091769 3000050 SCOP2B (2022-06-29)
ASCOP2B Superfamily2Fe-2S ferredoxin-like 8091771 3000113 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DSoxDe3ad8D1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: SoxDECOD (1.6)
CSoxGe3ad8C1 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: SoxGECOD (1.6)
BDAO_2nd_1e3ad8B2 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-C (From Topology)T: FAD-linked reductases-CF: DAO_2nd_1ECOD (1.6)
BFAD_binding_3_1ste3ad8B1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: FAD_binding_3_1stECOD (1.6)
AGCV_T_Ce3ad8A3 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Aminomethyltransferase beta-barrel domainF: GCV_T_CECOD (1.6)
AsoxAe3ad8A4 A: alpha arraysX: HTHH: bacterioferritin-associated ferredoxin (From Topology)T: bacterioferritin-associated ferredoxinF: soxAECOD (1.6)
AFer2_4e3ad8A5 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: Fer2_4ECOD (1.6)
AGCV_T_Ne3ad8A8 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: GCV_T_NECOD (1.6)
AGCV_T_N1e3ad8A7 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: GCV_T_N1ECOD (1.6)
AFAD_binding_3_1ste3ad8A6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: Nucleotide-binding domainF: FAD_binding_3_1stECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF04267Sarcosine oxidase, delta subunit family (SoxD)Sarcosine oxidase, delta subunit family- Family
PF04268Sarcosine oxidase, gamma subunit family (SoxG)Sarcosine oxidase, gamma subunit family- Family
PF01266FAD dependent oxidoreductase (DAO)FAD dependent oxidoreductaseThis family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1. Domain
PF17806Sarcosine oxidase A3 domain (SO_alpha_A3)Sarcosine oxidase A3 domainThis short domain is found in Heterotetrameric Sarcosine Oxidase's alpha A3 domain [1]. This domain binds to FMN in sarcosine oxidase. This domain is related to Pfam:PF04324 but lacks its iron binding cysteine residues. Domain
PF12831FAD dependent oxidoreductase (FAD_oxidored)FAD dependent oxidoreductase- Family
PF01571GCVT N-terminal domain (GCV_T)GCVT N-terminal domainThis entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical ...This entry represents the N-terminal domain in glycine cleavage T-proteins (GCVT) which are part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCVT proteins are involved in various biochemical processes, mainly on the degradation and transformation of small molecules. A significant function of these proteins is their role in the glycine cleavage system, which is responsible for the degradation of glycine. This system is composed of four proteins: P, T, L, and H. These proteins also participate in the demethylation of compounds such as N,N-dimethylglycine and sarcosine, converting them into simpler molecules like sarcosine and glycine, respectively. Additionally, they are involved in the catabolism of compounds like syringate and vanillate, contributing to the breakdown and assimilation of these molecules. GCVT proteins also include proteins that regulate enzymatic activity, such as the pyruvate dehydrogenase phosphatase regulatory subunit, which modulates sensitivity to magnesium ions [1-2].
Domain
PF135102Fe-2S iron-sulfur cluster binding domain (Fer2_4)2Fe-2S iron-sulfur cluster binding domainThe 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.
Domain
PF08669Glycine cleavage T-protein C-terminal barrel domain (GCV_T_C)Glycine cleavage T-protein C-terminal barrel domainThis is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl tran ...This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
SARCOSINE OXIDASE DELTA SUBUNIT
SARCOSINE OXIDASE GAMMA SUBUNIT
SARCOSINE OXIDASE BETA SUBUNIT
SARCOSINE OXIDASE ALPHA SUBUNIT