1nbi
From Proteopedia
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|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene> | |LIGAND= <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene> | ||
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Glycine_N-methyltransferase Glycine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.20 2.1.1.20] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_N-methyltransferase Glycine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.20 2.1.1.20] </span> |
|GENE= GNMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | |GENE= GNMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Rattus norvegicus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbi OCA], [http://www.ebi.ac.uk/pdbsum/1nbi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nbi RCSB]</span> | ||
}} | }} | ||
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[[Category: Takata, Y.]] | [[Category: Takata, Y.]] | ||
[[Category: Takusagawa, F.]] | [[Category: Takusagawa, F.]] | ||
| - | [[Category: SAM]] | ||
[[Category: catalytic mechanism]] | [[Category: catalytic mechanism]] | ||
[[Category: dynamical catalysis]] | [[Category: dynamical catalysis]] | ||
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[[Category: methyltransferase]] | [[Category: methyltransferase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:28:01 2008'' |
Revision as of 19:28, 30 March 2008
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| , resolution 3.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | GNMT (Rattus norvegicus) | ||||||
| Activity: | Glycine N-methyltransferase, with EC number 2.1.1.20 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.
Overview
Methyltransfer reactions are some of the most important reactions in biological systems. Glycine N-methyltransferase (GNMT) catalyzes the S-adenosyl-l-methionine- (SAM-) dependent methylation of glycine to form sarcosine. Unlike most SAM-dependent methyltransferases, GNMT has a relatively high value and is weakly inhibited by the product S-adenosyl-l-homocysteine (SAH). The major role of GNMT is believed to be the regulation of the cellular SAM/SAH ratio, which is thought to play a key role in SAM-dependent methyltransfer reactions. Crystal structures of GNMT complexed with SAM and acetate (a potent competitive inhibitor of Gly) and the R175K mutated enzyme complexed with SAM were determined at 2.8 and 3.0 A resolutions, respectively. With these crystal structures and the previously determined structures of substrate-free enzyme, a catalytic mechanism has been proposed. Structural changes occur in the transitions from the substrate-free to the binary complex and from the binary to the ternary complex. In the ternary complex stage, an alpha-helix in the N-terminus undergoes a major conformational change. As a result, the bound SAM is firmly connected to protein and a "Gly pocket" is created near the bound SAM. The second substrate Gly binds to Arg175 and is brought into the Gly pocket. Five hydrogen bonds connect the Gly in the proximity of the bound SAM and orient the lone pair orbital on the amino nitrogen (N) of Gly toward the donor methyl group (C(E)) of SAM. Thermal motion of the enzyme leads to a collision of the N and C(E) so that a S(N)2 methyltransfer reaction occurs. The proposed mechanism is supported by mutagenesis studies.
About this Structure
1NBI is a Single protein structure of sequence from Rattus norvegicus. Full crystallographic information is available from OCA.
Reference
Catalytic mechanism of glycine N-methyltransferase., Takata Y, Huang Y, Komoto J, Yamada T, Konishi K, Ogawa H, Gomi T, Fujioka M, Takusagawa F, Biochemistry. 2003 Jul 22;42(28):8394-402. PMID:12859184
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