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 67040 |
15428 57305 15428 57305 |
16680 57856 16680 57856 |
15611 57433 15611 57433 |
||||||
| PubChem |
34755 34755 |
5257127 750 5257127 750 |
25246222 439155 25246222 439155 |
1088 7311726 1088 7311726 |
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| 1bhjA01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1bhjB01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2cA01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2cB01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2gA01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2gB01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2hA01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2hB01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2hC01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2hD01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1xvaA01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1xvaB01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1kiaA01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1kiaB01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1kiaC01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1kiaD01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1nbhA01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1nbhB01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1nbhC01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1nbhD01 |
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Unbound | Analogue:ACT | Unbound | Unbound | |
| 1nbiA01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1nbiB01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1nbiC01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1nbiD01 |
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Unbound | Unbound | Unbound | Unbound | |
| 1bhjA02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1bhjB02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2cA02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2cB02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2gA02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2gB02 |
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Unbound | Unbound | Unbound | Unbound | |
| 1d2hA02 |
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Unbound | Unbound | Bound:SAH | Unbound | |
| 1d2hB02 |
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Unbound | Unbound | Bound:SAH | Unbound | |
| 1d2hC02 |
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Unbound | Unbound | Bound:SAH | Unbound | |
| 1d2hD02 |
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Unbound | Unbound | Bound:SAH | Unbound | |
| 1xvaA02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1xvaB02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1kiaA02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1kiaB02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1kiaC02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1kiaD02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbhA02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbhB02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbhC02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbhD02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbiA02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbiB02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbiC02 |
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Bound:SAM | Unbound | Unbound | Unbound | |
| 1nbiD02 |
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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 |
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TYR 194 | ||||
| 1bhjB01 |
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TYR 194 | ||||
| 1d2cA01 |
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TYR 194 | ||||
| 1d2cB01 |
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TYR 194 | ||||
| 1d2gA01 |
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TYR 194 | ||||
| 1d2gB01 |
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TYR 194 | ||||
| 1d2hA01 |
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TYR 194 | ||||
| 1d2hB01 |
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TYR 194 | ||||
| 1d2hC01 |
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TYR 194 | ||||
| 1d2hD01 |
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TYR 194 | ||||
| 1xvaA01 |
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TYR 194 | ||||
| 1xvaB01 |
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TYR 194 | ||||
| 1kiaA01 |
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TYR 194 | ||||
| 1kiaB01 |
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TYR 194 | ||||
| 1kiaC01 |
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TYR 194 | ||||
| 1kiaD01 |
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TYR 194 | ||||
| 1nbhA01 |
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TYR 194 | ||||
| 1nbhB01 |
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TYR 194 | ||||
| 1nbhC01 |
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TYR 194 | ||||
| 1nbhD01 |
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TYR 194 | ||||
| 1nbiA01 |
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TYR 194 | ||||
| 1nbiB01 |
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TYR 194 | ||||
| 1nbiC01 |
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TYR 194 | ||||
| 1nbiD01 |
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TYR 194 | ||||
| 1bhjA02 |
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GLY 137 | ||||
| 1bhjB02 |
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GLY 137 | ||||
| 1d2cA02 |
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GLY 137 | ||||
| 1d2cB02 |
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GLY 137 | ||||
| 1d2gA02 |
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GLY 137 | mutant R175K | |||
| 1d2gB02 |
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GLY 137 | mutant R175K | |||
| 1d2hA02 |
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GLY 137 | mutant R175K | |||
| 1d2hB02 |
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GLY 137 | mutant R175K | |||
| 1d2hC02 |
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GLY 137 | mutant R175K | |||
| 1d2hD02 |
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GLY 137 | mutant R175K | |||
| 1xvaA02 |
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GLY 137 | ||||
| 1xvaB02 |
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GLY 137 | ||||
| 1kiaA02 |
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GLY 137 | ||||
| 1kiaB02 |
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GLY 137 | ||||
| 1kiaC02 |
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GLY 137 | ||||
| 1kiaD02 |
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GLY 137 | ||||
| 1nbhA02 |
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GLY 137 | ||||
| 1nbhB02 |
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GLY 137 | ||||
| 1nbhC02 |
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GLY 137 | ||||
| 1nbhD02 |
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GLY 137 | ||||
| 1nbiA02 |
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GLY 137 | mutant R175K | |||
| 1nbiB02 |
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GLY 137 | mutant R175K | |||
| 1nbiC02 |
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GLY 137 | mutant R175K | |||
| 1nbiD02 |
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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, |
| 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, |
| 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 |