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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE GLYCINE N-METHYLTRANSFERASE (MONOCLINIC FORM)
 
Authors :  S. Pakhomova, Z. Luka, C. Wagner, M. E. Newcomer
Date :  28 Oct 03  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  A,B,C,D,E,F,G,H  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x)
Keywords :  Glycine N-Methyltransferase (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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINE N-METHYLTRANSFERASE
    Chains: A, B, C, D, E, F, G, H
    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

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH
Biological Unit 3 (1x): ABCDEFGH
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)G (1x)H (1x)
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1BME10Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1BME10Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 5 (1, 6)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:255 , GLY A:260 , CYS A:262BINDING SITE FOR RESIDUE BME A 1262
02AC2SOFTWAREARG A:175 , ASN A:176 , CYS A:282BINDING SITE FOR RESIDUE BME A 1282
03AC3SOFTWAREHIS B:55 , CYS B:57 , ASP B:131 , ARG B:165 , GLY B:167 , LYS E:190BINDING SITE FOR RESIDUE BME B 2057
04AC4SOFTWAREASN A:210 , CYS D:185 , ILE D:202 , THR D:204BINDING SITE FOR RESIDUE BME D 4185
05AC5SOFTWAREALA D:213 , CYS D:246BINDING SITE FOR RESIDUE BME D 4246
06AC6SOFTWARECYS D:262 , GLN D:263 , HIS D:264BINDING SITE FOR RESIDUE BME D 4262
07AC7SOFTWAREALA E:213 , CYS E:246BINDING SITE FOR RESIDUE BME E 5246
08AC8SOFTWARETYR F:179 , CYS F:282BINDING SITE FOR RESIDUE BME F 6282
09AC9SOFTWAREALA G:213 , CYS G:246BINDING SITE FOR RESIDUE BME G 7246
10BC1SOFTWAREASN G:176 , TYR G:179 , PRO G:281 , CYS G:282BINDING SITE FOR RESIDUE BME G 7282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R8Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1R8Y)

(-) 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:281
 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 d1r8ya_ A: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8yA01         1r8yA02 A:38-175,A:243-292 Vaccinia Virus protein VP39                                                                                    1r8yA01 A:22-37,A:176-242                                          1r8yA02 A:38-175,A:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhh.................eeeeeeee..eeeeeeeeeee.-----------.eeeeeee...hhhhhhhhhhhhh...eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y A   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQ-----------FSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 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  
                                                                                                                                                                                                                                                        223         235                                                         


Chain B from PDB  Type:PROTEIN  Length:282
 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 d1r8yb_ B: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8yB01         1r8yB02 B:38-175,B:243-292 Vaccinia Virus protein VP39                                                                                    1r8yB01 B:22-37,B:176-242                                          1r8yB02 B:38-175,B:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeee..----------.eeeeeee...hhhhhhhhhhhh....eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y B   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQV----------FSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 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        235                                                         


Chain C from PDB  Type:PROTEIN  Length:283
 aligned with GNMT_MOUSE | Q9QXF8 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:290
                                    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 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKK 291
               SCOP domains d1r8yc_ C: Glycine N-methyltransferase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------1r8yC01         1r8yC02 C:38-175,C:243-290 Vaccinia Virus protein VP39                                                                                    1r8yC01 C:22-37,C:176-242                                          1r8yC02 C:38-175,C:243-290                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeee.....-------.eeeeeee...hhhhhhhhhhhhh....eeeee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y C   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGT-------FSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKK 290
                                    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
                                                                                                                                                                                                                                                            227     235                                                       


Chain D from PDB  Type:PROTEIN  Length:286
 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 d1r8yd_ D: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------1r8yD01         1r8yD02 D:37-175,D:243-292 Vaccinia Virus protein VP39                                                                                     1r8yD01 D:21-36,D:176-242                                          1r8yD02 D:37-175,D:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh.................eeeeeeee..eeeeeeeeeeeee.------..eeeeeeeee...hhhhhhhhhhhhh...eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y D   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVP------SPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 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    232                                                            


Chain E from PDB  Type:PROTEIN  Length:286
 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 d1r8ye_ E: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------1r8yE01         1r8yE02 E:37-175,E:243-292 Vaccinia Virus protein VP39                                                                                     1r8yE01 E:21-36,E:176-242                                          1r8yE02 E:37-175,E:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeeee....------.eeeeeeee....hhhhhhhhhhhh......eee...............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y E   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGT------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  
                                                                                                                                                                                                                                                            227    234                                                          


Chain F from PDB  Type:PROTEIN  Length:282
 aligned with GNMT_MOUSE | Q9QXF8 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:291
                                    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 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGTGRDGSPGFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKT 292
               SCOP domains d1r8yf_ F: Glycine N-methyltransferase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------1r8yF01         1r8yF02 F:38-175,F:243-291 Vaccinia Virus protein VP39                                                                                    1r8yF01 F:22-37,F:176-242                                          1r8yF02 F:38-175,F:243-291                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh.................eeeeeeee..eeeeeeeeeee..---------..eeeeeee...hhhhhhhhhhhhh........................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y F   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQV---------GFSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKT 291
                                    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 G 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 d1r8yg_ G: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8yG01         1r8yG02 G:38-175,G:243-292 Vaccinia Virus protein VP39                                                                                    1r8yG01 G:22-37,G:176-242                                          1r8yG02 G:38-175,G:243-292                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhhh...............eeeeeeeeee..eeeeeeeeeee..---------..eeeeeee...hhhhhhhhhhhhh...eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y G   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 H from PDB  Type:PROTEIN  Length:282
 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 d1r8yh_ H: Glycine N-methyltransferase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------1r8yH01         1r8yH02 H:38-175,H:243-292 Vaccinia Virus protein VP39                                                                                    1r8yH01 H:22-37,H:176-242                                          1r8yH02 H:38-175,H:243-292                         CATH domains
           Pfam domains (1) ------------------------------------------------------Methyltransf_31-1r8yH01 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------Methyltransf_31-1r8yH02 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------Methyltransf_31-1r8yH03 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------Methyltransf_31-1r8yH04 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------Methyltransf_31-1r8yH05 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------Methyltransf_31-1r8yH06 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (6)
           Pfam domains (7) ------------------------------------------------------Methyltransf_31-1r8yH07 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (7)
           Pfam domains (8) ------------------------------------------------------Methyltransf_31-1r8yH08 H:55-223                                                                                                                                         --------------------------------------------------------------------- Pfam domains (8)
         Sec.struct. author .......................hhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhhhhh.eeee.hhhhhhhhh.....eeeeee..hhhhhh......hhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhh.................eeeeeeee..eeeeeeeeeee..----------.eeeeeee...hhhhhhhhhhhhh...eeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8y H   1 VDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVMSVDASDKMLKYALKERWNRRKEPSFDNWVIEEANWLTLDKDVLSGDGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRPGGLLVIDHRNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQV----------FSKFRLSYYPHCLASFTELVRAAFGGRCQHSVLGDFKPYKPGQAYVPCYFIHVLKKTD 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        235
   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, 8)

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

(-) CATH Domains  (2, 16)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 2-Layer Sandwich (8480)
(-)
Topology: Glycine N-methyltransferase; chain A, domain 1 (14)
(-)
Homologous Superfamily: Glycine N-methyltransferase, chain A, domain 1 (14)
(-)
House mouse (Mus musculus) (2)
1a1r8yD01D:21-36,D:176-242
1b1r8yE01E:21-36,E:176-242
1c1r8yC01C:22-37,C:176-242
1d1r8yF01F:22-37,F:176-242
1e1r8yG01G:22-37,G:176-242
1f1r8yB01B:22-37,B:176-242
1g1r8yH01H:22-37,H:176-242
1h1r8yA01A:22-37,A:176-242
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: Vaccinia Virus protein VP39 (378)
(-)
House mouse (Mus musculus) (3)
2a1r8yD02D:37-175,D:243-292
2b1r8yG02G:38-175,G:243-292
2c1r8yH02H:38-175,H:243-292
2d1r8yF02F:38-175,F:243-291
2e1r8yC02C:38-175,C:243-290
2f1r8yE02E:37-175,E:243-292
2g1r8yA02A:38-175,A:243-292
2h1r8yB02B:38-175,B:243-292

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (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

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

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        GNMT_MOUSE | Q9QXF8: 1r8x

(-) Related Entries Specified in the PDB File

1r8x CRYSTAL STRUCTURE OF MOUSE GLYCINE N-METHYLTRANSFERASE (TETRAGONAL FORM)