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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE GLYCINE N-METHYLTRANSFERASE (TETRAGONAL FORM)
 
Authors :  S. Pakhomova, Z. Luka, C. Wagner, M. E. Newcomer
Date :  28 Oct 03  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Glycine N-Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pakhomova, Z. Luka, S. Grohmann, C. Wagner, M. E. Newcomer
Glycine N-Methyltransferases: A Comparison Of The Crystal Structures And Kinetic Properties Of Recombinant Human, Mouse And Rat Enzymes.
Proteins V. 57 331 2004
PubMed-ID: 15340920  |  Reference-DOI: 10.1002/PROT.20209

(-) Compounds

Molecule 1 - GLYCINE N-METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B, PMME
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GNMT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1BME8Ligand/IonBETA-MERCAPTOETHANOL
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:144 , CYS A:146 , HIS A:214BINDING SITE FOR RESIDUE BME A 1146
2AC2SOFTWAREALA A:213 , CYS A:246BINDING SITE FOR RESIDUE BME A 1246
3AC3SOFTWAREASP A:62 , ALA A:64 , CYS A:65 , GLY A:66 , THR A:67 , ASP A:70 , LEU A:136 , SER A:139 , GLU B:15BINDING SITE FOR RESIDUE TRS A 1247
4AC4SOFTWARECYS B:146 , HIS B:214BINDING SITE FOR RESIDUE BME B 2146
5AC5SOFTWAREARG B:255 , GLY B:260 , CYS B:262 , HIS B:264BINDING SITE FOR RESIDUE BME B 2262
6AC6SOFTWAREGLU A:15 , ALA B:64 , CYS B:65 , GLY B:66 , THR B:67 , VAL B:69 , ASP B:70 , LEU B:136 , SER B:139BINDING SITE FOR RESIDUE TRS B 2263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R8X)

(-) Exons   (0, 0)

(no "Exon" information available for 1R8X)

(-) 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:283
 aligned with GNMT_MOUSE | Q9QXF8 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
           GNMT_MOUSE     2 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 293
               SCOP domains d1r8xa_ A: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8xA01         1r8xA02 A:38-175,A:243-292 Vaccinia Virus protein VP39                                                                                    1r8xA01 A:22-37,A:176-242                                          1r8xA02 A:38-175,A:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee...hhhhh......hhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeee..---------..eeeeeee...hhhhhhhhhhhh....eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8x A   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQV---------GFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   |     -   |   240       250       260       270       280       290  
                                                                                                                                                                                                                                                         224       234                                                          


Chain B from PDB  Type:PROTEIN  Length:284
 aligned with GNMT_MOUSE | Q9QXF8 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
           GNMT_MOUSE     2 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 293
               SCOP domains d1r8xb_ B: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8xB01         1r8xB02 B:38-175,B:243-292 Vaccinia Virus protein VP39                                                                                    1r8xB01 B:22-37,B:176-242                                          1r8xB02 B:38-175,B:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee....hhhhhh.....eeeeee...hhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeeee..--------.eeeeeeee...hhhhhhhhhhhhh....eeeee...............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8x B   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVP--------GFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    |    -   |   240       250       260       270       280       290  
                                                                                                                                                                                                                                                          225      234
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R8X)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GNMT_MOUSE | Q9QXF8)
molecular function
    GO:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0017174    glycine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine.
    GO:0016594    glycine binding    Interacting selectively and non-covalently with glycine, aminoethanoic acid.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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: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:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
    GO:0006555    methionine metabolic process    The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006111    regulation of gluconeogenesis    Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        GNMT_MOUSE | Q9QXF8: 1r8y

(-) Related Entries Specified in the PDB File

1r8y CRYSTAL STRUCTURE OF MOUSE GLYCINE N-METHYLTRANSFERASE (MONOCLINIC FORM)