DB code: D00075

CATH domain 3.30.46.10 : Glycine N-methyltransferase; chain A, domain 1 Catalytic domain
3.40.50.150 : Rossmann fold Catalytic domain
E.C. 2.1.1.20
CSA 1xva
M-CSA 1xva
MACiE M0023

CATH domain Related DB codes (homologues)
3.40.50.150 : Rossmann fold S00637 S00639 S00262 S00261 S00291 S00412 D00076 D00079 D00080 D00082 D00083 D00823

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq
P13255 Glycine N-methyltransferase
EC 2.1.1.20
Folate-binding protein
NP_058780.1 (Protein)
NM_017084.1 (DNA/RNA sequence)

KEGG enzyme name
glycine N-methyltransferase
glycine methyltransferase
S-adenosyl-L-methionine:glycine methyltransferase
GNMT

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13255 GNMT_RAT S-adenosyl-L-methionine + glycine = S- adenosyl-L-homocysteine + sarcosine. Homotetramer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00260 Glycine, serine and threonine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00019 C00037 C00021 C00213
E.C.
Compound S-Adenosyl-L-methionine Glycine S-Adenosyl-L-homocysteine Sarcosine
Type amino acids,amine group,nucleoside,sulfonium ion amino acids amino acids,amine group,nucleoside,sulfide group amino acids
ChEBI 67040
15428
57305
16680
57856
15611
57433
PubChem 34755
5257127
750
25246222
439155
1088
7311726
1bhjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bhjB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2hB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2hC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2hD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1xvaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1xvaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1kiaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1kiaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1kiaC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1kiaD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1nbhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1nbhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1nbhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1nbhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ACT Unbound Unbound
1nbiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1nbiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1nbiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1nbiD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bhjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1bhjB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1d2hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SAH Unbound
1d2hB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SAH Unbound
1d2hC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SAH Unbound
1d2hD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SAH Unbound
1xvaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1xvaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1kiaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1kiaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1kiaC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1kiaD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound
1nbiD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SAM Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bhjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1bhjB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2cA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2cB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2hB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2hC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1d2hD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1xvaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1xvaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1kiaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1kiaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1kiaC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1kiaD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbiC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1nbiD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 194
1bhjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1bhjB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1d2cA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1d2cB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1d2gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1d2gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1d2hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1d2hB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1d2hC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1d2hD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1xvaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1xvaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1kiaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1kiaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1kiaC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1kiaD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1nbhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1nbhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1nbhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1nbhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137
1nbiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1nbiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1nbiC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K
1nbiD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLY 137 mutant R175K

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.9, p.11992-11993 2
[3]
Fig.6, p.21 2
[7]
Fig.6, p.8399-8401

References
[1]
Resource
Comments
Medline ID
PubMed ID 7734248
Journal J Struct Biol
Year 1994
Volume 113
Pages 247-9
Authors Fu Z, Takusagawa F, Konishi K, Takata Y, Fujioka M
Title Crystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID 96406816
PubMed ID 8810903
Journal Biochemistry
Year 1996
Volume 35
Pages 11985-93
Authors Fu Z, Hu Y, Konishi K, Takata Y, Ogawa H, Gomi T, Fujioka M, Takusagawa F
Title Crystal structure of glycine N-methyltransferase from rat liver.
Related PDB 1xva
Related UniProtKB P13255
[3]
Resource
Comments
Medline ID
PubMed ID 9597750
Journal Int J Biochem Cell Biol
Year 1998
Volume 30
Pages 13-26
Authors Ogawa H, Gomi T, Takusagawa F, Fujioka M
Title Structure, function and physiological role of glycine N-methyltransferase.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID 98318042
PubMed ID 9655336
Journal Protein Sci
Year 1998
Volume 7
Pages 1326-31
Authors Pattanayek R, Newcomer ME, Wagner C
Title Crystal structure of apo-glycine N-methyltransferase (GNMT).
Related PDB 1bhj
Related UniProtKB P13255
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS)
Medline ID
PubMed ID 10756111
Journal J Mol Biol
Year 2000
Volume 298
Pages 149-62
Authors Huang Y, Komoto J, Konishi K, Takata Y, Ogawa H, Gomi T, Fujioka M, Takusagawa F
Title 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.
Related PDB 1d2c 1d2g 1d2h
Related UniProtKB P13255
[6]
Resource
Comments
Medline ID
PubMed ID 12079381
Journal J Mol Biol
Year 2002
Volume 320
Pages 223-35
Authors Komoto J, Huang Y, Takata Y, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F
Title Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12859184
Journal Biochemistry
Year 2003
Volume 42
Pages 8394-402
Authors Takata Y, Huang Y, Komoto J, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F
Title Catalytic mechanism of glycine N-methyltransferase.
Related PDB 1nbh 1nbi
Related UniProtKB

Comments

Created Updated
2004-03-17 2009-02-26