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(-) Description

Title :  GUANIDINOACETATE METHYLTRANSFERASE
 
Authors :  J. Komoto, F. Takusagawa
Date :  12 Apr 03  (Deposition) - 29 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Guanidinoacetate Methyltransferase, Methyltransferase, S- Adenosylhomocysteine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Komoto, Y. Takata, T. Yamada, K. Konishi, H. Ogawa, T. Gomi, M. Fujioka, F. Takusagawa
Monoclinic Guanidinoacetate Methyltransferase And Gadolinium Ion-Binding Characteristics.
Acta Crystallogr. , Sect. D V. 59 1589 2003
PubMed-ID: 12925789  |  Reference-DOI: 10.1107/S0907444903014719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANIDINOACETATE N-METHYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.1.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGAMT
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:49 , GLY A:67 , PHE A:68 , GLY A:69 , MET A:70 , ALA A:71 , ILE A:72 , ALA A:73 , GLU A:89 , CYS A:90 , GLY A:114 , LEU A:115 , TRP A:116 , GLU A:117 , ASP A:134 , TYR A:136BINDING SITE FOR RESIDUE SAH A 4001
2AC2SOFTWAREALA A:217 , ASP A:218 , MET B:49 , GLY B:67 , PHE B:68 , GLY B:69 , MET B:70 , ALA B:71 , ILE B:72 , ALA B:73 , GLU B:89 , CYS B:90 , GLY B:114 , LEU B:115 , TRP B:116 , GLU B:117 , ASP B:134 , LEU B:138BINDING SITE FOR RESIDUE SAH B 4002
3AC3SOFTWAREMET C:49 , GLY C:67 , PHE C:68 , GLY C:69 , MET C:70 , ALA C:71 , ILE C:72 , ALA C:73 , GLU C:89 , CYS C:90 , GLY C:114 , LEU C:115 , TRP C:116 , GLU C:117 , ASP C:134 , TYR C:136 , HOH C:5025 , HOH C:5103BINDING SITE FOR RESIDUE SAH C 4003
4AC4SOFTWAREMET D:49 , GLY D:67 , PHE D:68 , GLY D:69 , MET D:70 , ALA D:71 , ILE D:72 , ALA D:73 , GLU D:89 , CYS D:90 , GLY D:114 , LEU D:115 , TRP D:116 , GLU D:117 , ASP D:134 , TYR D:136BINDING SITE FOR RESIDUE SAH D 4004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P1B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P1B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P1B)

(-) Exons   (0, 0)

(no "Exon" information available for 1P1B)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:193
 aligned with GAMT_RAT | P10868 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:193
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
             GAMT_RAT    44 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEEAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 236
               SCOP domains d1p1ba_ A: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1p1bA00 A:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.....eeeee.hhhhhhhhh....eeeeeee............hhhhhhhhhhhheeeeeeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p1b A  43 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 235
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with GAMT_RAT | P10868 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:193
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
             GAMT_RAT    44 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEEAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 236
               SCOP domains d1p1bb_ B: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1p1bB00 B:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.....eeeee.hhhhhhhhh....eeeeee.....hhhhh.hhhhhhhhhhhhhheeeeeeeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p1b B  43 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 235
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   

Chain C from PDB  Type:PROTEIN  Length:193
 aligned with GAMT_RAT | P10868 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:193
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
             GAMT_RAT    44 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEEAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 236
               SCOP domains d1p1bc_ C: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1p1bC00 C:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeeeee.hhhhhhhhhhhhh.....eeeee.hhhhhhhhh....eeeeeee............hhhhhhhhhhhheeeeeeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p1b C  43 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 235
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   

Chain D from PDB  Type:PROTEIN  Length:193
 aligned with GAMT_RAT | P10868 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:193
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
             GAMT_RAT    44 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEEAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 236
               SCOP domains d1p1bd_ D: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1p1bD00 D:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhhh..eeeeeeee.hhhhhhhhhhhhh.....eeeee.hhhhhhhhh....eeeeeee............hhhhhhhhhhhheeeeeeeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p1b D  43 RWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH 235
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P1B)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GAMT_RAT | P10868)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0030731    guanidinoacetate N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine + H(+).
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0046498    S-adenosylhomocysteine metabolic process    The chemical reactions and pathways involving S-adenosylhomocysteine; the L-enantiomer is formed from S-adenosylmethionine and is a strong inhibitor of S-adenosylmethionine-mediated methylation reactions. It can be cleaved to form adenosine and homocysteine.
    GO:0046500    S-adenosylmethionine metabolic process    The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
    GO:0006601    creatine biosynthetic process    The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle.
    GO:1990402    embryonic liver development    The process occurring during the embryonic phase whose specific outcome is the progression of the liver over time, from its formation to the mature structure.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GAMT_RAT | P108681khh 1p1c 1xcj 1xcl

(-) Related Entries Specified in the PDB File

1p1c GUANIDINOACETATE METHYLTRANSFERASE WITH GD ION