D00075
type: Enzyme
cath: Glycine N-methyltransferase; chain A, domain 1
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/2.1.1.20
csa: 1xva
macie: M0023
uniprot: P13255
kegg enzyme: glycine N-methyltransferase
kegg enzyme: glycine methyltransferase
kegg enzyme: S-adenosyl-L-methionine:glycine methyltransferase
kegg enzyme: GNMT
kegg pathway: Glycine, serine and threonine metabolism
kegg substrate: S-Adenosyl-L-methionine
kegg substrate: Glycine
kegg product: S-Adenosyl-L-homocysteine
kegg product: Sarcosine
pdb: 1bhjA01
pdb: 1bhjB01
pdb: 1d2cA01
pdb: 1d2cB01
pdb: 1d2gA01
pdb: 1d2gB01
pdb: 1d2hA01
pdb: 1d2hB01
pdb: 1d2hC01
pdb: 1d2hD01
pdb: 1xvaA01
pdb: 1xvaB01
pdb: 1kiaA01
pdb: 1kiaB01
pdb: 1kiaC01
pdb: 1kiaD01
pdb: 1nbhA01
pdb: 1nbhB01
pdb: 1nbhC01
pdb: 1nbhD01
pdb: 1nbiA01
pdb: 1nbiB01
pdb: 1nbiC01
pdb: 1nbiD01
pdb: 1bhjA02
pdb: 1bhjB02
pdb: 1d2cA02
pdb: 1d2cB02
pdb: 1d2gA02
pdb: 1d2gB02
pdb: 1d2hA02
pdb: 1d2hB02
pdb: 1d2hC02
pdb: 1d2hD02
pdb: 1xvaA02
pdb: 1xvaB02
pdb: 1kiaA02
pdb: 1kiaB02
pdb: 1kiaC02
pdb: 1kiaD02
pdb: 1nbhA02
pdb: 1nbhB02
pdb: 1nbhC02
pdb: 1nbhD02
pdb: 1nbiA02
pdb: 1nbiB02
pdb: 1nbiC02
pdb: 1nbiD02
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1bhjA01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1bhjB01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2cA01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2cB01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2gA01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2gB01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2hA01
pdb bound state: Unbound
  compound: S-Adenosyl-L-methionine
  pdb: 1d2hB01
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/D00075#8
references: Crystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.
references: Crystal structure of glycine N-methyltransferase from rat liver.
references: Structure, function and physiological role of glycine N-methyltransferase.
references: Crystal structure of apo-glycine N-methyltransferase (GNMT).
references: Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.
references: Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.
references: Catalytic mechanism of glycine N-methyltransferase.

Glycine N-methyltransferase; chain A, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.30.46.10
catalytic domain: index.html

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.150
catalytic domain: index.html

Glycine, serine and threonine metabolism
type: KeggPathway
references: KEGG:MAP00260

S-Adenosyl-L-methionine
type: KeggSubstrate
references: KEGG:C00019
compound type: amino acids
compound type: amine group
compound type: nucleoside
compound type: sulfonium ion
references: CHEBI:67040
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Glycine
type: KeggSubstrate
references: KEGG:C00037
compound type: amino acids
references: CHEBI:15428
references: CHEBI:57305
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

S-Adenosyl-L-homocysteine
type: KeggProduct
references: KEGG:C00021
compound type: amino acids
compound type: amine group
compound type: nucleoside
compound type: sulfide group
references: CHEBI:16680
references: CHEBI:57856
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Sarcosine
type: KeggProduct
references: KEGG:C00213
compound type: amino acids
references: CHEBI:15611
references: CHEBI:57433
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1bhjA01
type: Pdb
references: 1bhj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bhj
catalytic residue: TYR 194

1bhjB01
type: Pdb
references: 1bhj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bhj
catalytic residue: TYR 194

1d2cA01
type: Pdb
references: 1d2c
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2c
catalytic residue: TYR 194

1d2cB01
type: Pdb
references: 1d2c
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2c
catalytic residue: TYR 194

1d2gA01
type: Pdb
references: 1d2g
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2g
catalytic residue: TYR 194

1d2gB01
type: Pdb
references: 1d2g
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2g
catalytic residue: TYR 194

1d2hA01
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
catalytic residue: TYR 194

1d2hB01
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
catalytic residue: TYR 194

1d2hC01
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
catalytic residue: TYR 194

1d2hD01
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
catalytic residue: TYR 194

1xvaA01
type: Pdb
references: 1xva
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1xva
catalytic residue: TYR 194

1xvaB01
type: Pdb
references: 1xva
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1xva
catalytic residue: TYR 194

1kiaA01
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
catalytic residue: TYR 194

1kiaB01
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
catalytic residue: TYR 194

1kiaC01
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
catalytic residue: TYR 194

1kiaD01
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
catalytic residue: TYR 194

1nbhA01
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
catalytic residue: TYR 194

1nbhB01
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
catalytic residue: TYR 194

1nbhC01
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
catalytic residue: TYR 194

1nbhD01
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
catalytic residue: TYR 194

1nbiA01
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
catalytic residue: TYR 194

1nbiB01
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
catalytic residue: TYR 194

1nbiC01
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
catalytic residue: TYR 194

1nbiD01
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
catalytic residue: TYR 194

1bhjA02
type: Pdb
references: 1bhj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bhj
main chain in catalysis: GLY 137

1bhjB02
type: Pdb
references: 1bhj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bhj
main chain in catalysis: GLY 137

1d2cA02
type: Pdb
references: 1d2c
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2c
main chain in catalysis: GLY 137

1d2cB02
type: Pdb
references: 1d2c
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2c
main chain in catalysis: GLY 137

1d2gA02
type: Pdb
references: 1d2g
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2g
main chain in catalysis: GLY 137
comment: mutant R175K

1d2gB02
type: Pdb
references: 1d2g
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2g
main chain in catalysis: GLY 137
comment: mutant R175K

1d2hA02
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
main chain in catalysis: GLY 137
comment: mutant R175K

1d2hB02
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
main chain in catalysis: GLY 137
comment: mutant R175K

1d2hC02
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
main chain in catalysis: GLY 137
comment: mutant R175K

1d2hD02
type: Pdb
references: 1d2h
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d2h
main chain in catalysis: GLY 137
comment: mutant R175K

1xvaA02
type: Pdb
references: 1xva
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1xva
main chain in catalysis: GLY 137

1xvaB02
type: Pdb
references: 1xva
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1xva
main chain in catalysis: GLY 137

1kiaA02
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
main chain in catalysis: GLY 137

1kiaB02
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
main chain in catalysis: GLY 137

1kiaC02
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
main chain in catalysis: GLY 137

1kiaD02
type: Pdb
references: 1kia
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1kia
main chain in catalysis: GLY 137

1nbhA02
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
main chain in catalysis: GLY 137

1nbhB02
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
main chain in catalysis: GLY 137

1nbhC02
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
main chain in catalysis: GLY 137

1nbhD02
type: Pdb
references: 1nbh
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbh
main chain in catalysis: GLY 137

1nbiA02
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
main chain in catalysis: GLY 137
comment: mutant R175K

1nbiB02
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
main chain in catalysis: GLY 137
comment: mutant R175K

1nbiC02
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
main chain in catalysis: GLY 137
comment: mutant R175K

1nbiD02
type: Pdb
references: 1nbi
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nbi
main chain in catalysis: GLY 137
comment: mutant R175K

Crystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7734248
journal: J Struct Biol
volume: 113
pages: 247-9
published year: 1994
authors:
  item: Fu Z
  item: Takusagawa F
  item: Konishi K
  item: Takata Y
  item: Fujioka M

Crystal structure of glycine N-methyltransferase from rat liver.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
medline id: 96406816
references: http://www.ncbi.nlm.nih.gov/pubmed/8810903
journal: Biochemistry
volume: 35
pages: 11985-93
published year: 1996
authors:
  item: Fu Z
  item: Hu Y
  item: Konishi K
  item: Takata Y
  item: Ogawa H
  item: Gomi T
  item: Fujioka M
  item: Takusagawa F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P13255

Structure, function and physiological role of glycine N-methyltransferase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9597750
journal: Int J Biochem Cell Biol
volume: 30
pages: 13-26
published year: 1998
authors:
  item: Ogawa H
  item: Gomi T
  item: Takusagawa F
  item: Fujioka M

Crystal structure of apo-glycine N-methyltransferase (GNMT).
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
medline id: 98318042
references: http://www.ncbi.nlm.nih.gov/pubmed/9655336
journal: Protein Sci
volume: 7
pages: 1326-31
published year: 1998
authors:
  item: Pattanayek R
  item: Newcomer ME
  item: Wagner C
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P13255

Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS)
references: http://www.ncbi.nlm.nih.gov/pubmed/10756111
journal: J Mol Biol
volume: 298
pages: 149-62
published year: 2000
authors:
  item: Huang Y
  item: Komoto J
  item: Konishi K
  item: Takata Y
  item: Ogawa H
  item: Gomi T
  item: Fujioka M
  item: Takusagawa F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P13255

Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12079381
journal: J Mol Biol
volume: 320
pages: 223-35
published year: 2002
authors:
  item: Komoto J
  item: Huang Y
  item: Takata Y
  item: Yamada T
  item: Konishi K
  item: Ogawa H
  item: Gomi T
  item: Fujioka M
  item: Takusagawa F

Catalytic mechanism of glycine N-methyltransferase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12859184
journal: Biochemistry
volume: 42
pages: 8394-402
published year: 2003
authors:
  item: Takata Y
  item: Huang Y
  item: Komoto J
  item: Yamada T
  item: Konishi K
  item: Ogawa H
  item: Gomi T
  item: Fujioka M
  item: Takusagawa F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Analogue
compound: Glycine
pdb: 1xvaA01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1xvaB01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1kiaA01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1kiaB01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1kiaC01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1kiaD01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1nbhA01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1nbhB01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1nbhC01
ligand het code: ACT

Analogue
compound: Glycine
pdb: 1nbhD01
ligand het code: ACT

ReferenceForCatalyticMechanism
reference index: 2
reference section: Fig.9, p.11992-11993
reference step: 2

ReferenceForCatalyticMechanism
reference index: 3
reference section: Fig.6, p.21
reference step: 2

ReferenceForCatalyticMechanism
reference index: 7
reference section: Fig.6, p.8399-8401