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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT)
 
Authors :  R. Pattanayek, M. E. Newcomer, C. Wagner
Date :  09 Jun 98  (Deposition) - 06 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Methyltransferase, Folate Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pattanayek, M. E. Newcomer, C. Wagner
Crystal Structure Of Apo-Glycine N-Methyltransferase (Gnmt)
Protein Sci. V. 7 1326 1998
PubMed-ID: 9655336

(-) Compounds

Molecule 1 - GLYCINE N-METHYLTRANSFERASE
    Cell Line: BL21
    Chains: A, B
    EC Number: 2.1.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: APO FORM
    Synonym: GNMT, FOLATE BINDING PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1BHJ)

(-) Sites  (0, 0)

(no "Site" information available for 1BHJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000223071ENSRNOE00000155790chr9:10127092-10127301210GNMT_RAT1-69692A:1-68
B:1-68		68
68
1.2ENSRNOT000000223072ENSRNOE00000156216chr9:10128745-10128872128GNMT_RAT69-112442A:68-111
B:68-111		44
44
1.3ENSRNOT000000223073ENSRNOE00000156616chr9:10129429-10129539111GNMT_RAT112-149382A:111-148
B:111-148		38
38
1.4ENSRNOT000000223074ENSRNOE00000157087chr9:10129733-10129875143GNMT_RAT149-196482A:148-195
B:148-195		48
48
1.5ENSRNOT000000223075ENSRNOE00000157394chr9:10129963-10130084122GNMT_RAT197-237412A:196-236
B:196-236		41
41
1.6ENSRNOT000000223076ENSRNOE00000157770chr9:10130171-10130444274GNMT_RAT237-293572A:236-292
B:236-292		57
57

(-) 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:292
 aligned with GNMT_RAT | P13255 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_RAT     2 VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG 293
               SCOP domains d1bhja_ A: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1bhjA01         1bhjA02 A:38-175,A:243-292 Vaccinia Virus protein VP39                                                                                    1bhjA01 A:22-37,A:176-242                                          1bhjA02 A:38-175,A:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhh.........hhhhhhhhhhhhh....eeee........hhhhhh...eeee....hhhhhhhhhhhhh....hhhhh..........hhh.........eeee...hhhh........hhhhhhhhhhhh......eeeeeee.hhhhhhh................eeeeeeeeee..eeeeeeeeeeeee.........eeeeeeeee....hhhhhhhhhhhh......eee...............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-68 UniProt: 1-69 [INCOMPLETE]                    ------------------------------------------Exon 1.3  PDB: A:111-148              -----------------------------------------------Exon 1.5  PDB: A:196-236 UniProt: 197-237-------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.2  PDB: A:68-111 UniProt: 69-112     ------------------------------------Exon 1.4  PDB: A:148-195 UniProt: 149-196       ----------------------------------------Exon 1.6  PDB: A:236-292 UniProt: 237-293                 Transcript 1 (2)
                 1bhj A   1 VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290  


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with GNMT_RAT | P13255 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_RAT     2 VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG 293
               SCOP domains d1bhjb_ B: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1bhjB01         1bhjB02 B:38-175,B:243-292 Vaccinia Virus protein VP39                                                                                    1bhjB01 B:22-37,B:176-242                                          1bhjB02 B:38-175,B:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhh........hhhhhhhhhhhhhh...eeee......hhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh.hhhhh.eeee.....hhh.........eeee...hhhh........hhhhhhhhhhhhh.....eeeeeee.hhhhhhh..................eeeeeeee..eeeeeeeeeeeee.........eeeeeeeee....hhhhhhhhhhhh........................eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-68 UniProt: 1-69 [INCOMPLETE]                    ------------------------------------------Exon 1.3  PDB: B:111-148              -----------------------------------------------Exon 1.5  PDB: B:196-236 UniProt: 197-237-------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.2  PDB: B:68-111 UniProt: 69-112     ------------------------------------Exon 1.4  PDB: B:148-195 UniProt: 149-196       ----------------------------------------Exon 1.6  PDB: B:236-292 UniProt: 237-293                 Transcript 1 (2)
                 1bhj B   1 VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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 1BHJ)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GNMT_RAT | P13255)
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: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:0098603    selenol Se-methyltransferase activity    Catalysis of the reaction: R + Se-Adenosylselenomethionine => CH3-R + Se-Adenosyl-L-selenohomocysteine.
    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:0046655    folic acid metabolic process    The chemical reactions and pathways involving 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:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:1901052    sarcosine metabolic process    The chemical reactions and pathways involving sarcosine.
    GO:0001887    selenium compound metabolic process    The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        GNMT_RAT | P13255: 1d2c 1d2g 1d2h 1kia 1nbh 1nbi 1xva 2idj 2idk 3thr 3ths

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BHJ)