1PJ5 | pdb_00001pj5

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1pj5a1 All beta proteins Elongation factor/aminomethyltransferase common domain Aminomethyltransferase beta-barrel domain Aminomethyltransferase beta-barrel domain N,N-dimethylglycine oxidase, C-terminal domain (Arthrobacter globiformis ) [TaxId: 1665 ], SCOPe (2.08)
Ad1pj5a2 Alpha and beta proteins (a/b) FAD/NAD(P)-binding domain FAD/NAD(P)-binding domain FAD-linked reductases, N-terminal domain N,N-dimethylglycine oxidase (Arthrobacter globiformis ) [TaxId: 1665 ], SCOPe (2.08)
Ad1pj5a3 Alpha and beta proteins (a+b) FAD-linked reductases, C-terminal domain FAD-linked reductases, C-terminal domain L-aminoacid/polyamine oxidase N,N-dimethylglycine oxidase (Arthrobacter globiformis ) [TaxId: 1665 ], SCOPe (2.08)
Ad1pj5a4 Alpha and beta proteins (a+b) Folate-binding domain Folate-binding domain Aminomethyltransferase folate-binding domain N,N-dimethylglycine oxidase domain 3 (Arthrobacter globiformis ) [TaxId: 1665 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyAmine oxidase-like 8001437 4000128 SCOP2 (2022-06-29)
ASCOP2 FamilyGcvT aminomethyltransferase-like 8001438 4000062 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyFlavoreductase-like 8017496 3000055 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyFolate-binding domain-like 8001552 3000025 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyAminomethyltransferase beta-barrel domain-like 8056079 3000024 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGCV_T_Ce1pj5A1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Aminomethyltransferase beta-barrel domainF: GCV_T_CECOD (1.6)
AKOG2844e1pj5A3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: FAD-linked reductases-C (From Topology)T: FAD-linked reductases-CF: KOG2844ECOD (1.6)
AGCV_T_Ne1pj5A6 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_N1e1pj5A5 A: a+b two layersX: Alpha-beta plaitsH: Aminomethyltransferase folate-binding domain (From Topology)T: Aminomethyltransferase folate-binding domainF: GCV_T_N1ECOD (1.6)
ADAO_1ste1pj5A4 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: DAO_1stECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.50.50.60 Alpha Beta 3-Layer(bba) Sandwich FAD/NAD(P)-binding domain FAD/NAD(P)-binding domainCATH (4.3.0)
A3.30.9.10 Alpha Beta 2-Layer Sandwich D-Amino Acid Oxidase Chain A, domain 2CATH (4.3.0)
A3.30.1360.120 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
A3.30.70.1400 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Aminomethyltransferase beta-barrel domainsCATH (4.3.0)
A2.40.30.110 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF16350FAD dependent oxidoreductase central domain (FAO_M)FAD dependent oxidoreductase central domain- 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
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
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
N,N-dimethylglycine oxidase - -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR013977Aminomethyltransferase, C-terminal domainDomain
IPR028896Aminomethyltransferase-likeFamily
IPR027266Aminomethyltransferase superfamilyHomologous Superfamily
IPR032503FAD dependent oxidoreductase, central domainDomain
IPR029043Glycine cleavage T-protein/YgfZ, C-terminalHomologous Superfamily
IPR006076FAD dependent oxidoreductaseDomain
IPR036188FAD/NAD(P)-binding domain superfamilyHomologous Superfamily
IPR006222GCVT, N-terminal domainDomain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
dimethylglycine oxidase (tetrahydrofolate utilising)  M-CSA #879

Catalyses the oxidative demethylation of N,N-dimethylglycine to yield sarcosine, 5,10-methylenetetrahydrofolate and hydrogen peroxide. The oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channelling mechanism. This channelling occurs by non-biased diffusion of the iminium intermediate through a large solvent cavity connecting active site 1 (N-terminus) and active site 2 (C-terminus). The synthesis of 5,10-methylenetetrahydrofolate (at active site 2) prevents the accumulation of formaldehyde (not shown), formed by hydrolysis of the iminium intermediate product (at active site 1).

Defined by 3 residues: HIS:A-225TYR:A-259ASP:A-552
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Explore in 3D: M-CSA Motif Definition
Extent of motif is too large to support Structure Motif searching.
EC: 1.5.3.10 (PDB Primary Data)