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PDBsum entry 1p1b

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1p1b
Jmol
Contents
Protein chains
193 a.a. *
Ligands
SAH ×4
Waters ×150
* Residue conservation analysis
PDB id:
1p1b
Name: Transferase
Title: Guanidinoacetate methyltransferase
Structure: Guanidinoacetate n-methyltransferase. Chain: a, b, c, d. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: gamt. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.214     R-free:   0.269
Authors: J.Komoto,F.Takusagawa
Key ref:
J.Komoto et al. (2003). Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics. Acta Crystallogr D Biol Crystallogr, 59, 1589-1596. PubMed id: 12925789 DOI: 10.1107/S0907444903014719
Date:
12-Apr-03     Release date:   29-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P10868  (GAMT_RAT) -  Guanidinoacetate N-methyltransferase
Seq:
Struc:
236 a.a.
193 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
=
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!
  Biochemical function     guanidinoacetate N-methyltransferase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444903014719 Acta Crystallogr D Biol Crystallogr 59:1589-1596 (2003)
PubMed id: 12925789  
 
 
Monoclinic guanidinoacetate methyltransferase and gadolinium ion-binding characteristics.
J.Komoto, Y.Takata, T.Yamada, 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. Recombinant rat liver GAMT truncated at amino acid 37 from the N-terminus has been crystallized with S-adenosylhomocysteine (SAH) in a monoclinic modification and the crystal structure has been determined at 2.8 A resolution. There are two dimers in the crystallographic asymmetric unit. Each dimer has non-crystallographic twofold symmetry and is related to the other dimer by pseudo-4(3) symmetry along the crystallographic b axis. The overall structure of GAMT crystallized in the monoclinic modification is quite similar to the structure observed in the tetragonal modification [Komoto et al. (2002), J. Mol. Biol. 320, 223-235], with the exception of the loop containing Tyr136. In the monoclinic modification, the loops in three of the four subunits have a catalytically unfavorable conformation and the loop of the fourth subunit has a catalytically favorable conformation as observed in the crystals of the tetragonal modification. From the structures in the monoclinic and tetragonal modifications, we can explain why the Y136F mutant enzyme retains considerable catalytic activity while the Y136V mutant enzyme loses the catalytic activity. The crystal structure of a Gd derivative of the tetragonal modification has also been determined. By comparing the Gd-derivative structure with the native structures in the tetragonal and the monoclinic modifications, useful characteristic features of Gd-ion binding for application in protein crystallography have been observed. Gd ions can bind to proteins without changing the native protein structures and Gd atoms produce strong anomalous dispersion signals from Cu Kalpha radiation; however, Gd-ion binding to protein requires a relatively specific geometry.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 GAMT catalytic reaction.
Figure 3.
Figure 3 (a) Superimposed view of two polypeptides from residues 132-150 of subunits A and B. The polypeptides that belong to subunit A and B are illustrated in aquamarine and light pink, respectively. (b) Superimposed view of two polypeptides from residues 134-137 of subunits A and B with the bound SAH and Arg220' of the partner subunit. The same color codes are applied. Figs. 3-, 4-and 5-were produced using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1589-1596) copyright 2003.  
  Figures were selected by an automated process.