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(-) Description

Title :  CRYSTAL STRUCTURE OF GUANIDINOACETATE METHYLTRANSFERASE FROM RAT LIVER: A TEMPLATE STRUCTURE OF PROTEIN ARGININE METHYLTRANSFERASE
 
Authors :  F. Takusagawa, J. Komoto
Date :  30 Nov 01  (Deposition) - 12 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Creatine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Komoto, Y. Huang, Y. Takata, T. Yamada, K. Konishi, H. Ogawa, T. Gomi, M. Fujioka, F. Takusagawa
Crystal Structure Of Guanidinoacetate Methyltransferase From Rat Liver: A Model Structure Of Protein Arginine Methyltransferase.
J. Mol. Biol. V. 320 223 2002
PubMed-ID: 12079381  |  Reference-DOI: 10.1016/S0022-2836(02)00448-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANIDINOACETATE METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL TRUNCATION
    Organ: LIVER
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GUANIDINOACETATE N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
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 , LEU A:115 , TRP A:116 , GLU A:117 , ASP A:134 , THR A:135 , TYR A:136BINDING SITE FOR RESIDUE SAH A 236
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 , THR B:135 , TYR B:136BINDING SITE FOR RESIDUE SAH B 1236

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KHH)

(-) Sequences/Alignments

Asymmetric/Biological 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 d1khha_ A: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1khhA00 A:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....eeeeee.hhhhhhhhh....eeeeee...........hhhhhhhhhhhhhheeeeeeeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khh 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 d1khhb_ B: Guanidinoacetate methyltransferase                                                                                                                                                     SCOP domains
               CATH domains 1khhB00 B:43-235 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeee....hhhhhhhh...eeeeeeee.hhhhhhhhhhhhh....eeeeee.hhhhhhhhh....eeeeee.....hhhhh.hhhhhhhhhhhhhheeeeeeeee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khh B  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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        GAMT_RAT | P10868: 1p1b 1p1c 1xcj 1xcl

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