3THR
Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005542 | molecular_function | folic acid binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0005977 | biological_process | glycogen metabolic process |
| A | 0006111 | biological_process | regulation of gluconeogenesis |
| A | 0006544 | biological_process | glycine metabolic process |
| A | 0006555 | biological_process | methionine metabolic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0008757 | molecular_function | S-adenosylmethionine-dependent methyltransferase activity |
| A | 0016594 | molecular_function | glycine binding |
| A | 0017174 | molecular_function | glycine N-methyltransferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0034708 | cellular_component | methyltransferase complex |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0046498 | biological_process | S-adenosylhomocysteine metabolic process |
| A | 0046500 | biological_process | S-adenosylmethionine metabolic process |
| A | 0051289 | biological_process | protein homotetramerization |
| A | 0098603 | molecular_function | selenol Se-methyltransferase activity |
| A | 1901052 | biological_process | sarcosine metabolic process |
| A | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
| B | 0005542 | molecular_function | folic acid binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005977 | biological_process | glycogen metabolic process |
| B | 0006111 | biological_process | regulation of gluconeogenesis |
| B | 0006544 | biological_process | glycine metabolic process |
| B | 0006555 | biological_process | methionine metabolic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0008757 | molecular_function | S-adenosylmethionine-dependent methyltransferase activity |
| B | 0016594 | molecular_function | glycine binding |
| B | 0017174 | molecular_function | glycine N-methyltransferase activity |
| B | 0032259 | biological_process | methylation |
| B | 0034708 | cellular_component | methyltransferase complex |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0046498 | biological_process | S-adenosylhomocysteine metabolic process |
| B | 0046500 | biological_process | S-adenosylmethionine metabolic process |
| B | 0051289 | biological_process | protein homotetramerization |
| B | 0098603 | molecular_function | selenol Se-methyltransferase activity |
| B | 1901052 | biological_process | sarcosine metabolic process |
| B | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
| C | 0005542 | molecular_function | folic acid binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0005977 | biological_process | glycogen metabolic process |
| C | 0006111 | biological_process | regulation of gluconeogenesis |
| C | 0006544 | biological_process | glycine metabolic process |
| C | 0006555 | biological_process | methionine metabolic process |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0008168 | molecular_function | methyltransferase activity |
| C | 0008757 | molecular_function | S-adenosylmethionine-dependent methyltransferase activity |
| C | 0016594 | molecular_function | glycine binding |
| C | 0017174 | molecular_function | glycine N-methyltransferase activity |
| C | 0032259 | biological_process | methylation |
| C | 0034708 | cellular_component | methyltransferase complex |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0046498 | biological_process | S-adenosylhomocysteine metabolic process |
| C | 0046500 | biological_process | S-adenosylmethionine metabolic process |
| C | 0051289 | biological_process | protein homotetramerization |
| C | 0098603 | molecular_function | selenol Se-methyltransferase activity |
| C | 1901052 | biological_process | sarcosine metabolic process |
| C | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
| D | 0005542 | molecular_function | folic acid binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0005977 | biological_process | glycogen metabolic process |
| D | 0006111 | biological_process | regulation of gluconeogenesis |
| D | 0006544 | biological_process | glycine metabolic process |
| D | 0006555 | biological_process | methionine metabolic process |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0008168 | molecular_function | methyltransferase activity |
| D | 0008757 | molecular_function | S-adenosylmethionine-dependent methyltransferase activity |
| D | 0016594 | molecular_function | glycine binding |
| D | 0017174 | molecular_function | glycine N-methyltransferase activity |
| D | 0032259 | biological_process | methylation |
| D | 0034708 | cellular_component | methyltransferase complex |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0046498 | biological_process | S-adenosylhomocysteine metabolic process |
| D | 0046500 | biological_process | S-adenosylmethionine metabolic process |
| D | 0051289 | biological_process | protein homotetramerization |
| D | 0098603 | molecular_function | selenol Se-methyltransferase activity |
| D | 1901052 | biological_process | sarcosine metabolic process |
| D | 1904047 | molecular_function | S-adenosyl-L-methionine binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE C2F A 1100 |
| Chain | Residue |
| A | TYR5 |
| B | ARG239 |
| C | SER3 |
| C | VAL4 |
| C | TYR5 |
| D | LEU207 |
| D | HIS214 |
| D | MET215 |
| A | THR7 |
| A | HOH642 |
| A | HOH653 |
| A | HOH670 |
| A | HOH698 |
| B | LEU207 |
| B | HIS214 |
| B | THR217 |
| site_id | AC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE TAM A 1500 |
| Chain | Residue |
| A | TRP30 |
| A | TYR33 |
| A | ILE34 |
| A | THR37 |
| A | GLY137 |
| A | SER139 |
| A | HIS142 |
| A | HOH416 |
| A | HOH487 |
| A | HOH671 |
| B | ALA13 |
| B | GLU15 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE C2F B 1700 |
| Chain | Residue |
| B | TYR279 |
| B | VAL280 |
| B | CYS282 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE C2F C 1410 |
| Chain | Residue |
| C | ARG59 |
| C | PRO125 |
| C | ALA126 |
| C | HOH316 |
| C | HOH405 |
| C | HOH427 |
| C | HOH585 |
| C | HOH635 |
| C | HOH648 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE TAM C 1600 |
| Chain | Residue |
| C | TRP30 |
| C | TYR33 |
| C | ILE34 |
| C | THR37 |
| C | MET90 |
| C | GLY137 |
| C | HOH337 |
| C | HOH437 |
| C | HOH519 |
| C | HOH639 |
| D | ALA13 |
| D | GLU15 |
| D | HOH387 |
| site_id | AC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE C2F D 1200 |
| Chain | Residue |
| A | LEU207 |
| A | HIS214 |
| A | MET215 |
| B | SER3 |
| B | VAL4 |
| B | TYR5 |
| C | LEU207 |
| C | HIS214 |
| C | MET215 |
| C | THR217 |
| C | ARG239 |
| C | HOH317 |
| D | TYR5 |
| D | THR7 |
| D | HOH369 |
| D | HOH627 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE TAM D 1400 |
| Chain | Residue |
| C | GLU15 |
| D | TYR33 |
| D | ILE34 |
| D | MET90 |
| D | GLY137 |
| D | ASN191 |
| D | HOH345 |
| D | HOH382 |
| D | HOH402 |
| D | HOH444 |
| D | HOH522 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22037183, ECO:0000312|PDB:3THR, ECO:0000312|PDB:3THS |
| Chain | Residue | Details |
| B | HIS214 | |
| B | ARG239 | |
| C | SER3 | |
| C | HIS214 | |
| C | ARG239 | |
| D | SER3 | |
| D | HIS214 | |
| D | ARG239 | |
| A | ARG239 | |
| B | SER3 | |
| A | SER3 | |
| A | HIS214 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22037183, ECO:0000312|PDB:3THS |
| Chain | Residue | Details |
| C | TYR5 | |
| D | TYR5 | |
| A | TYR5 | |
| B | TYR5 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0007744|PDB:1NBH |
| Chain | Residue | Details |
| C | TYR21 | |
| D | TYR21 | |
| A | TYR21 | |
| B | TYR21 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0007744|PDB:1NBH, ECO:0007744|PDB:1NBI |
| Chain | Residue | Details |
| C | TRP30 | |
| C | ARG40 | |
| C | ASP85 | |
| C | ASN116 | |
| D | TRP30 | |
| D | ARG40 | |
| D | ASP85 | |
| D | ASN116 | |
| A | ASN116 | |
| B | TRP30 | |
| B | ARG40 | |
| B | ASP85 | |
| B | ASN116 | |
| A | TRP30 | |
| A | ARG40 | |
| A | ASP85 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:8810903, ECO:0007744|PDB:1XVA |
| Chain | Residue | Details |
| B | ARG175 | |
| B | TYR220 | |
| C | TYR33 | |
| C | ARG175 | |
| C | TYR220 | |
| D | TYR33 | |
| D | ARG175 | |
| D | TYR220 | |
| B | TYR33 | |
| A | TYR33 | |
| A | ARG175 | |
| A | TYR220 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0000269|PubMed:8810903, ECO:0000312|PDB:1XVA, ECO:0007744|PDB:1NBH, ECO:0007744|PDB:1NBI |
| Chain | Residue | Details |
| B | ALA64 | |
| C | ALA64 | |
| D | ALA64 | |
| A | ALA64 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0000269|PubMed:8810903, ECO:0007744|PDB:1NBI, ECO:0007744|PDB:1XVA |
| Chain | Residue | Details |
| C | LEU136 | |
| D | LEU136 | |
| A | LEU136 | |
| B | LEU136 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylvaline => ECO:0000269|PubMed:2822402 |
| Chain | Residue | Details |
| A | VAL1 | |
| B | VAL1 | |
| C | VAL1 | |
| D | VAL1 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q9QXF8 |
| Chain | Residue | Details |
| A | SER9 | |
| B | SER9 | |
| C | SER9 | |
| D | SER9 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9QXF8 |
| Chain | Residue | Details |
| A | TYR33 | |
| B | TYR33 | |
| C | TYR33 | |
| D | TYR33 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9QXF8 |
| Chain | Residue | Details |
| A | LYS45 | |
| A | LYS190 | |
| A | LYS195 | |
| A | LYS200 | |
| B | LYS45 | |
| B | LYS190 | |
| B | LYS195 | |
| B | LYS200 | |
| C | LYS45 | |
| C | LYS190 | |
| C | LYS195 | |
| C | LYS200 | |
| D | LYS45 | |
| D | LYS190 | |
| D | LYS195 | |
| D | LYS200 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 23 |
| Chain | Residue | Details |
| A | TYR21 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| A | GLY137 | electrostatic stabiliser, hydrogen bond acceptor |
| A | HIS142 | activator |
| A | ARG175 | electrostatic stabiliser |
| A | TYR194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 5 |
| Details | M-CSA 23 |
| Chain | Residue | Details |
| B | TYR21 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| B | GLY137 | electrostatic stabiliser, hydrogen bond acceptor |
| B | HIS142 | activator |
| B | ARG175 | electrostatic stabiliser |
| B | TYR194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 5 |
| Details | M-CSA 23 |
| Chain | Residue | Details |
| C | TYR21 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| C | GLY137 | electrostatic stabiliser, hydrogen bond acceptor |
| C | HIS142 | activator |
| C | ARG175 | electrostatic stabiliser |
| C | TYR194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 5 |
| Details | M-CSA 23 |
| Chain | Residue | Details |
| D | TYR21 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| D | GLY137 | electrostatic stabiliser, hydrogen bond acceptor |
| D | HIS142 | activator |
| D | ARG175 | electrostatic stabiliser |
| D | TYR194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
