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PDBsum entry 1d2h

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1d2h
Jmol
Contents
Protein chains
252 a.a. *
Ligands
SAH ×4
Waters ×508
* Residue conservation analysis
PDB id:
1d2h
Name: Transferase
Title: Crystal structure of r175k mutant glycine n- methyltransferase complexed with s-adenosylhomocysteine
Structure: Glycine n-methyltransferase. Chain: a, b, c, d. Fragment: whole enzyme. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Tissue: liver. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.195     R-free:   0.247
Authors: Y.Huang,J.Komoto,F.Takusagawa,K.Konishi,Y.Takata
Key ref:
Y.Huang et al. (2000). 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. J Mol Biol, 298, 149-162. PubMed id: 10756111 DOI: 10.1006/jmbi.2000.3637
Date:
11-Oct-99     Release date:   25-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13255  (GNMT_RAT) -  Glycine N-methyltransferase
Seq:
Struc:
293 a.a.
252 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.20  - Glycine N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
S-adenosyl-L-methionine
+ glycine
=
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ sarcosine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     methylation   8 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3637 J Mol Biol 298:149-162 (2000)
PubMed id: 10756111  
 
 
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.
Y.Huang, J.Komoto, K.Konishi, Y.Takata, H.Ogawa, T.Gomi, M.Fujioka, F.Takusagawa.
 
  ABSTRACT  
 
Glycine N-methyltransferase (S-adenosyl-l-methionine: glycine methyltransferase, EC 2.1.1.20; GNMT) catalyzes the AdoMet-dependent methylation of glycine to form sarcosine (N-methylglycine). Unlike most methyltransferases, GNMT is a tetrameric protein showing a positive cooperativity in AdoMet binding and weak inhibition by S-adenosylhomocysteine (AdoHcy). The first crystal structure of GNMT complexed with AdoMet showed a unique "closed" molecular basket structure, in which the N-terminal section penetrates and corks the entrance of the adjacent subunit. Thus, the apparent entrance or exit of the active site is not recognizable in the subunit structure, suggesting that the enzyme must possess a second, enzymatically active, "open" structural conformation. A new crystalline form of the R175K enzyme has been grown in the presence of an excess of AdoHcy, and its crystal structure has been determined at 3.0 A resolution. In this structure, the N-terminal domain (40 amino acid residues) of each subunit has moved out of the active site of the adjacent subunit, and the entrances of the active sites are now opened widely. An AdoHcy molecule has entered the site occupied in the "closed" structure by Glu15 and Gly16 of the N-terminal domain of the adjacent subunit. An AdoHcy binds to the consensus AdoMet binding site observed in the other methyltransferase. This AdoHcy binding site supports the glycine binding site (Arg175) deduced from a chemical modification study and site-directed mutagenesis (R175K). The crystal structures of WT and R175K enzymes were also determined at 2.5 A resolution. These enzyme structures have a closed molecular basket structure and are isomorphous to the previously determined AdoMet-GNMT structure. By comparing the open structure to the closed structure, mechanisms for auto-inhibition and for the forced release of the product AdoHcy have been revealed in the GNMT structure. The N-terminal section of the adjacent subunit occupies the AdoMet binding site and thus inhibits the methyltransfer reaction, whereas the same N-terminal section forces the departure of the potentially potent inhibitor AdoHcy from the active site and thus facilitates the methyltransfer reaction. Consequently GNMT is less active at a low level of AdoMet concentration, and is only weakly inhibited by AdoHcy. These properties of GNMT are particularly suited for regulation of the cellular AdoMet/AdoHcy ratio.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Subunit structures in (a) R175K closed structure and (b) AdoHcy-R175K open structure. The N-terminal domain, C-terminal domain and S-domain are illustrated by red, cyan and green, respectively. The U-loop of the adjacent subunit is shown by thick magenta coil. In the open structure, the N-terminal domain is invisible and an AdoHcy molecule (red) binds to the consensus AdoMet-binding site.
Figure 7.
Figure 7. Schematic diagrams of interaction of AdoHcy in the active site. It is noted that Trp117 stacks with the adenine ring.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 149-162) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382027 K.Rutherford, and V.Daggett (2010).
Polymorphisms and disease: hotspots of inactivation in methyltransferases.
  Trends Biochem Sci, 35, 531-538.  
19483083 Z.Luka, S.H.Mudd, and C.Wagner (2009).
Glycine N-methyltransferase and regulation of S-adenosylmethionine levels.
  J Biol Chem, 284, 22507-22511.  
17334902 M.A.Grillo, and S.Colombatto (2008).
S-adenosylmethionine and its products.
  Amino Acids, 34, 187-193.  
17158459 Z.Luka, S.Pakhomova, L.V.Loukachevitch, M.Egli, M.E.Newcomer, and C.Wagner (2007).
5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase.
  J Biol Chem, 282, 4069-4075.
PDB codes: 2idj 2idk
17660255 Z.Luka, S.Pakhomova, Y.Luka, M.E.Newcomer, and C.Wagner (2007).
Destabilization of human glycine N-methyltransferase by H176N mutation.
  Protein Sci, 16, 1957-1964.
PDB code: 2azt
15340920 S.Pakhomova, Z.Luka, S.Grohmann, C.Wagner, and M.E.Newcomer (2004).
Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes.
  Proteins, 57, 331-337.
PDB codes: 1r74 1r8x 1r8y
12826405 H.L.Schubert, R.M.Blumenthal, and X.Cheng (2003).
Many paths to methyltransfer: a chronicle of convergence.
  Trends Biochem Sci, 28, 329-335.  
12466265 R.Waditee, Y.Tanaka, K.Aoki, T.Hibino, H.Jikuya, J.Takano, T.Takabe, and T.Takabe (2003).
Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica.
  J Biol Chem, 278, 4932-4942.  
11847284 C.D.Smith, M.Carson, A.M.Friedman, M.M.Skinner, L.Delucas, L.Chantalat, L.Weise, T.Shirasawa, and D.Chattopadhyay (2002).
Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.
  Protein Sci, 11, 625-635.
PDB code: 1i1n
11472630 J.M.Bujnicki, M.Feder, M.Radlinska, and L.Rychlewski (2001).
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
  BMC Bioinformatics, 2, 2.
PDB code: 1ic3
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11080641 M.M.Skinner, J.M.Puvathingal, R.L.Walter, and A.M.Friedman (2000).
Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
  Structure, 8, 1189-1201.
PDB code: 1dl5
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.