EzCatDB: D00075

DB codeD00075
CATH domainDomain 13.30.46.10Catalytic domain
Domain 23.40.50.150Catalytic domain
E.C.2.1.1.20
CSA1xva
MACiEM0023

CATH domainRelated DB codes (homologues)
3.40.50.150S00637,S00639,S00262,S00261,S00291,S00412,D00076,D00079,D00080,D00082,D00083,D00823

Enzyme Name
Swiss-protKEGG

P13255
Protein nameGlycine N-methyltransferaseglycine N-methyltransferase
glycine methyltransferase
S-adenosyl-L-methionine:glycine methyltransferase
GNMT
SynonymsEC 2.1.1.20
Folate-binding protein

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism

Swiss-prot:Accession NumberP13255
Entry nameGNMT_RAT
ActivityS-adenosyl-L-methionine + glycine = S- adenosyl-L-homocysteine + sarcosine.
SubunitHomotetramer.
Subcellular locationCytoplasm.
Cofactor


SubstratesProducts
KEGG-idC00019C00037C00021C00213
CompoundS-Adenosyl-L-methionineGlycineS-Adenosyl-L-homocysteineSarcosine
Typeamino acids,amine group,nucleoside,sulfonium ionamino acidsamino acids,amine group,nucleoside,sulfide groupamino acids
1bhjA01UnboundUnboundUnboundUnbound
1bhjB01UnboundUnboundUnboundUnbound
1d2cA01UnboundUnboundUnboundUnbound
1d2cB01UnboundUnboundUnboundUnbound
1d2gA01UnboundUnboundUnboundUnbound
1d2gB01UnboundUnboundUnboundUnbound
1d2hA01UnboundUnboundUnboundUnbound
1d2hB01UnboundUnboundUnboundUnbound
1d2hC01UnboundUnboundUnboundUnbound
1d2hD01UnboundUnboundUnboundUnbound
1xvaA01UnboundAnalogue:ACTUnboundUnbound
1xvaB01UnboundAnalogue:ACTUnboundUnbound
1kiaA01UnboundAnalogue:ACTUnboundUnbound
1kiaB01UnboundAnalogue:ACTUnboundUnbound
1kiaC01UnboundAnalogue:ACTUnboundUnbound
1kiaD01UnboundAnalogue:ACTUnboundUnbound
1nbhA01UnboundAnalogue:ACTUnboundUnbound
1nbhB01UnboundAnalogue:ACTUnboundUnbound
1nbhC01UnboundAnalogue:ACTUnboundUnbound
1nbhD01UnboundAnalogue:ACTUnboundUnbound
1nbiA01UnboundUnboundUnboundUnbound
1nbiB01UnboundUnboundUnboundUnbound
1nbiC01UnboundUnboundUnboundUnbound
1nbiD01UnboundUnboundUnboundUnbound
1bhjA02UnboundUnboundUnboundUnbound
1bhjB02UnboundUnboundUnboundUnbound
1d2cA02UnboundUnboundUnboundUnbound
1d2cB02UnboundUnboundUnboundUnbound
1d2gA02UnboundUnboundUnboundUnbound
1d2gB02UnboundUnboundUnboundUnbound
1d2hA02UnboundUnboundBound:SAHUnbound
1d2hB02UnboundUnboundBound:SAHUnbound
1d2hC02UnboundUnboundBound:SAHUnbound
1d2hD02UnboundUnboundBound:SAHUnbound
1xvaA02Bound:SAMUnboundUnboundUnbound
1xvaB02Bound:SAMUnboundUnboundUnbound
1kiaA02Bound:SAMUnboundUnboundUnbound
1kiaB02Bound:SAMUnboundUnboundUnbound
1kiaC02Bound:SAMUnboundUnboundUnbound
1kiaD02Bound:SAMUnboundUnboundUnbound
1nbhA02Bound:SAMUnboundUnboundUnbound
1nbhB02Bound:SAMUnboundUnboundUnbound
1nbhC02Bound:SAMUnboundUnboundUnbound
1nbhD02Bound:SAMUnboundUnboundUnbound
1nbiA02Bound:SAMUnboundUnboundUnbound
1nbiB02Bound:SAMUnboundUnboundUnbound
1nbiC02Bound:SAMUnboundUnboundUnbound
1nbiD02Bound:SAMUnboundUnboundUnbound

Active-site residues
resource
literature [7]
pdbCatalytic residuesMain-chain involved in catalysiscomment
1bhjA01TYR 194


1bhjB01TYR 194


1d2cA01TYR 194


1d2cB01TYR 194


1d2gA01TYR 194


1d2gB01TYR 194


1d2hA01TYR 194


1d2hB01TYR 194


1d2hC01TYR 194


1d2hD01TYR 194


1xvaA01TYR 194


1xvaB01TYR 194


1kiaA01TYR 194


1kiaB01TYR 194


1kiaC01TYR 194


1kiaD01TYR 194


1nbhA01TYR 194


1nbhB01TYR 194


1nbhC01TYR 194


1nbhD01TYR 194


1nbiA01TYR 194


1nbiB01TYR 194


1nbiC01TYR 194


1nbiD01TYR 194


1bhjA02
GLY 137

1bhjB02
GLY 137

1d2cA02
GLY 137

1d2cB02
GLY 137

1d2gA02
GLY 137
mutant R175K
1d2gB02
GLY 137
mutant R175K
1d2hA02
GLY 137
mutant R175K
1d2hB02
GLY 137
mutant R175K
1d2hC02
GLY 137
mutant R175K
1d2hD02
GLY 137
mutant R175K
1xvaA02
GLY 137

1xvaB02
GLY 137

1kiaA02
GLY 137

1kiaB02
GLY 137

1kiaC02
GLY 137

1kiaD02
GLY 137

1nbhA02
GLY 137

1nbhB02
GLY 137

1nbhC02
GLY 137

1nbhD02
GLY 137

1nbiA02
GLY 137
mutant R175K
1nbiB02
GLY 137
mutant R175K
1nbiC02
GLY 137
mutant R175K
1nbiD02
GLY 137
mutant R175K

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.9, p.11992-119932
[3]Fig.6, p.212
[7]Fig.6, p.8399-8401

references
[1]
PubMed ID7734248
JournalJ Struct Biol
Year1994
Volume113
Pages247-9
AuthorsFu Z, Takusagawa F, Konishi K, Takata Y, Fujioka M
TitleCrystallization and preliminary X-ray diffraction studies of glycine methyltransferase from rat liver.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID96406816
PubMed ID8810903
JournalBiochemistry
Year1996
Volume35
Pages11985-93
AuthorsFu Z, Hu Y, Konishi K, Takata Y, Ogawa H, Gomi T, Fujioka M, Takusagawa F
TitleCrystal structure of glycine N-methyltransferase from rat liver.
Related PDB1xva
Related Swiss-protP13255
[3]
PubMed ID9597750
JournalInt J Biochem Cell Biol
Year1998
Volume30
Pages13-26
AuthorsOgawa H, Gomi T, Takusagawa F, Fujioka M
TitleStructure, function and physiological role of glycine N-methyltransferase.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID98318042
PubMed ID9655336
JournalProtein Sci
Year1998
Volume7
Pages1326-31
AuthorsPattanayek R, Newcomer ME, Wagner C
TitleCrystal structure of apo-glycine N-methyltransferase (GNMT).
Related PDB1bhj
Related Swiss-protP13255
[5]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS)
PubMed ID10756111
JournalJ Mol Biol
Year2000
Volume298
Pages149-62
AuthorsHuang Y, Komoto J, Konishi K, Takata Y, Ogawa H, Gomi T, Fujioka M, Takusagawa F
TitleMechanisms 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 PDB1d2c,1d2g,1d2h
Related Swiss-protP13255
[6]
PubMed ID12079381
JournalJ Mol Biol
Year2002
Volume320
Pages223-35
AuthorsKomoto J, Huang Y, Takata Y, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F
TitleCrystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.
[7]
PubMed ID12859184
JournalBiochemistry
Year2003
Volume42
Pages8394-402
AuthorsTakata Y, Huang Y, Komoto J, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F
TitleCatalytic mechanism of glycine N-methyltransferase.
Related PDB1nbh,1nbi


createdupdated
2004-03-172009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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