Annotations: 1XVA

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xvaa_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Glycine N-methyltransferase	Glycine N-methyltransferase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1xvab_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Glycine N-methyltransferase	Glycine N-methyltransferase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glycine N-methyltransferase	8019898	4000664	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032278	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032278	3000118	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF13649	e1xvaA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13649	ECOD (1.6)
B	PF13649	e1xvaB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13649	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.46.10	Alpha Beta	2-Layer Sandwich	Glycine N-methyltransferase	chain A, domain 1	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.30.46.10	Alpha Beta	2-Layer Sandwich	Glycine N-methyltransferase	chain A, domain 1	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13649	Methyltransferase domain (Methyltransf_25)	Methyltransferase domain	This family appears to be a methyltransferase domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	GLYCINE N-METHYLTRANSFERASE	cation binding organic acid binding binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity cation binding organic acid binding binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity selenol Se-methyltransferase activity N-methyltransferase activity glycine N-methyltransferase activity amide binding modified amino acid binding vitamin binding organic cyclic compound binding folic acid binding heterocyclic compound binding S-adenosyl-L-methionine binding sulfur compound binding identical protein binding protein binding	monosaccharide metabolic process gluconeogenesis regulation of primary metabolic process organic substance metabolic process regulation of small molecule metabolic process organic substance biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide metabolic process gluconeogenesis regulation of primary metabolic process organic substance metabolic process regulation of small molecule metabolic process organic substance biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process biosynthetic process regulation of gluconeogenesis metabolic process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process organonitrogen compound metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process cellular process one-carbon metabolic process sarcosine metabolic process cellular modified amino acid metabolic process non-proteinogenic amino acid metabolic process methylation protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis glycosyl compound metabolic process carbohydrate derivative metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process sulfur compound metabolic process purine ribonucleoside metabolic process S-adenosylhomocysteine metabolic process nucleoside metabolic process purine-containing compound metabolic process organic cyclic compound metabolic process purine nucleoside metabolic process ribonucleoside metabolic process S-adenosylmethionine metabolic process sulfur amino acid metabolic process aspartate family amino acid metabolic process methionine metabolic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glucan metabolic process polysaccharide metabolic process energy reserve metabolic process macromolecule metabolic process	protein-containing complex intracellular anatomical structure catalytic complex methyltransferase complex transferase complex cellular anatomical entity cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR014369	Glycine/Sarcosine N-methyltransferase	Family
A, B	IPR041698	Methyltransferase domain 25	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	glycine N-methyltransferase M-CSA #23	Glycine N-methyltransferase (GNMT) isolated from Rattus norvegicus catalyses the transfer of a methyl group from S-adenosyl-methionine (SAM) to glycine to produce N-methylglycine (sarcosine) and S-adenosyl homocysteine (SAH). Unlike most SAM-dependent methyltransferases, GNMT is not strongly inhibited by SAH. This, coupled with no evidence of a physiological role for sarcosine, has led to the suggestion that GNMT plays a key role in modulating the SAM/SAH ratio in tissues where it is an important cofactor, and so controls methyltransferase activity. GNMT exists as a dimer of dimers. Each subunit contains a molecular basket structure and a flexible N-terminal U-loop that can block the entrance to the basket of the partner subunit of the dimer. The U-loop competes with SAM for binding at the active site and so can regulate catalytic activity. GNMT binds first to SAM, which causes a conformational change, and then to glycine.	Defined by 5 residues: TYR:A-21GLY:A-137HIS:A-142ARG:A-175TYR:A-194 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.20 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.20

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 R01GM133198.