spacer
spacer

PDBsum entry 1xcj

Go to PDB code: 
protein ligands links
Transferase PDB id
1xcj
Jmol
Contents
Protein chain
229 a.a. *
Ligands
SAH
NMG
Waters ×60
* Residue conservation analysis
PDB id:
1xcj
Name: Transferase
Title: Guanidinoacetate methyltransferase containing s- adenosylhomocysteine and guanidinoacetate
Structure: Guanidinoacetate n-methyltransferase. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Tissue: liver. Gene: gamt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.224     R-free:   0.279
Authors: J.Komoto,T.Yamada,Y.Takata,F.Takusagawa
Key ref:
J.Komoto et al. (2004). Catalytic mechanism of guanidinoacetate methyltransferase: crystal structures of guanidinoacetate methyltransferase ternary complexes. Biochemistry, 43, 14385-14394. PubMed id: 15533043 DOI: 10.1021/bi0486785
Date:
02-Sep-04     Release date:   07-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P10868  (GAMT_RAT) -  Guanidinoacetate N-methyltransferase
Seq:
Struc:
236 a.a.
229 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.2  - Guanidinoacetate N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Creatine Biosynthesis
      Reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine
S-adenosyl-L-methionine
+
guanidinoacetate
Bound ligand (Het Group name = NMG)
corresponds exactly
=
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ creatine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     methylation   4 terms 
  Biochemical function     transferase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0486785 Biochemistry 43:14385-14394 (2004)
PubMed id: 15533043  
 
 
Catalytic mechanism of guanidinoacetate methyltransferase: crystal structures of guanidinoacetate methyltransferase ternary complexes.
J.Komoto, T.Yamada, Y.Takata, K.Konishi, H.Ogawa, T.Gomi, M.Fujioka, F.Takusagawa.
 
  ABSTRACT  
 
Guanidinoacetate methyltransferase (GAMT) is the enzyme that catalyzes the last step of creatine biosynthesis. The enzyme is found in abundance in the livers of all vertebrates. The intact GAMT from recombinant rat liver has been crystallized with an inhibitor S-adenosylhomocysteine (SAH) and a substrate guanidinoacetate (GAA), and with SAH and an inhibitor guanidine (GUN). These ternary complex structures have been determined at 2.0 A resolution. GAMT has an alpha/beta open-sandwich structure, and the N-terminal section (residues 1-42) covers the active site entrance so that the active site is not visible. SAH has extensive interactions with GAMT through H-bonds and hydrophobic interactions. The guanidino groups of GAA and GUN form two pairs of H-bonds with E45 and D134, respectively. The carboxylate group of GAA interacts with the backbone amide groups of L170 and T171. A model structure of GAMT containing the two substrates (SAM and GAA) was built by attaching a methyl group (C(E)) on S(D) of the bound SAH. On the basis of this model structure, a catalytic mechanism of GAMT is proposed. The active site entrance is opened when the N-terminal section is moved out. GAA and SAM enter the active site and interact with the amino acid residues on the surface of the active site by polar and nonpolar interactions. O(D1) of D134 and C(E) of SAM approach N(E) of GAA from the tetrahedral directions. The O(D1)...N(E) and C(E)...N(E) distances are 2.9 and 2.2 A, respectively. It is proposed that three slightly negatively charged carbonyl oxygen atoms (O of T135, O of C168, and O(B) of GAA) around O(D1) of D134 increase the pK(a) of O(D1) so that O(D1) abstracts the proton on N(E). A strong nucleophile is generated on the deprotonated N(E) of GAA, which abstracts the methyl group (C(E)) from the positively charged S(D) of SAM, and creatine (methyl-GAA) and SAH (demethyl-SAM) are produced. E45, D134, and Y221 mutagenesis studies support the proposed mechanism. A mutagenesis study and the inhibitory mechanism of guanidine analogues support the proposed mechanism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20372740 D.O'Hagan, and J.W.Schmidberger (2010).
Enzymes that catalyse SN2 reaction mechanisms.
  Nat Prod Rep, 27, 900-918.  
19739191 H.Deng, S.A.McMahon, A.S.Eustáquio, B.S.Moore, J.H.Naismith, and D.O'Hagan (2009).
Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62).
  Chembiochem, 10, 2455-2459.
PDB code: 2wr8
19570037 N.Drinkwater, C.L.Gee, M.Puri, K.R.Criscione, M.J.McLeish, G.L.Grunewald, and J.L.Martin (2009).
Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity.
  Biochem J, 422, 463-471.
PDB codes: 3hca 3hcb 3hcc 3hcd 3hce 3hcf
19733262 P.Georgieva, Q.Wu, M.J.McLeish, and F.Himo (2009).
The reaction mechanism of phenylethanolamine N-methyltransferase: a density functional theory study.
  Biochim Biophys Acta, 1794, 1831-1837.  
19389626 R.Shi, S.S.Lamb, B.Zakeri, A.Proteau, Q.Cui, T.Sulea, A.Matte, G.D.Wright, and M.Cygler (2009).
Structure and function of the glycopeptide N-methyltransferase MtfA, a tool for the biosynthesis of modified glycopeptide antibiotics.
  Chem Biol, 16, 401-410.
PDB codes: 3g2m 3g2o 3g2p 3g2q
17713745 C.S.Xu, and C.F.Chang (2008).
Expression profiles of the genes associated with metabolism and transport of amino acids and their derivatives in rat liver regeneration.
  Amino Acids, 34, 91.  
17053070 X.Zhang, and T.C.Bruice (2006).
Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise.
  Proc Natl Acad Sci U S A, 103, 16141-16146.  
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 code is shown on the right.