4PAA | pdb_00004paa

Crystal structure of the mature form of rat DMGDH complexed with tetrahydrofolate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	POLH-Rev1_HhH	e4paaB2	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: POLH-Rev1_HhH	ECOD (v294.1)
B	DAO, NAD_binding_8, FAO_M	e4paaB4	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DAO, NAD_binding_8, FAO_M	ECOD (v294.1)
B	Carot_N	e4paaB5	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Carot_N	ECOD (v294.1)
A	POLH-Rev1_HhH	e4paaA1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: POLH-Rev1_HhH	ECOD (v294.1)
A	DAO, NAD_binding_8, FAO_M	e4paaA5	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DAO, NAD_binding_8, FAO_M	ECOD (v294.1)
A	Carot_N	e4paaA4	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Carot_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
B	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
B	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
A	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF16350	FAD dependent oxidoreductase central domain (FAO_M)	FAD dependent oxidoreductase central domain	-	Family
A, B	PF01571	GCVT N-terminal domain (GCV_T)	GCVT N-terminal domain	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 ...	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
A, B	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This 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
A, B	PF08669	Glycine cleavage T-protein C-terminal barrel domain (GCV_T_C)	Glycine cleavage T-protein C-terminal barrel domain	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 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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Dimethylglycine dehydrogenase	vitamin binding organic acid binding binding ion binding modified amino acid binding folic acid binding anion binding carboxylic acid binding heterocyclic compound binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding nucleotide binding oxidoreductase activity vitamin binding organic acid binding binding ion binding modified amino acid binding folic acid binding anion binding carboxylic acid binding heterocyclic compound binding small molecule binding flavin adenine dinucleotide binding nucleoside phosphate binding nucleotide binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors dimethylglycine dehydrogenase activity catalytic activity oxidoreductase activity, acting on the CH-NH group of donors, flavin as acceptor	choline metabolic process metabolic process cellular process folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process catabolic process amino-acid betaine catabolic process modified amino acid catabolic process amino-acid betaine metabolic process choline metabolic process metabolic process cellular process folic acid-containing compound metabolic process tetrahydrofolate interconversion modified amino acid metabolic process small molecule metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process one-carbon metabolic process catabolic process amino-acid betaine catabolic process modified amino acid catabolic process amino-acid betaine metabolic process amine metabolic process choline catabolic process biogenic amine catabolic process amine catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR028896	Aminomethyltransferase-like	Family
A, B	IPR013977	Aminomethyltransferase, C-terminal domain	Domain
A, B	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR006222	GCVT, N-terminal domain	Domain
A, B	IPR032503	FAD dependent oxidoreductase, central domain	Domain
A, B	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A, B	IPR006076	FAD dependent oxidoreductase	Domain

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.