1D2H
CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE
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 | 8 |
Details | BINDING SITE FOR RESIDUE SAH A 1301 |
Chain | Residue |
A | ASP85 |
A | ALA86 |
A | SER87 |
A | MET90 |
A | ASN116 |
A | TRP117 |
A | SER139 |
A | HIS142 |
site_id | AC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SAH B 2301 |
Chain | Residue |
B | VAL69 |
B | ASP85 |
B | SER87 |
B | MET90 |
B | ASN116 |
B | TRP117 |
B | SER139 |
B | ALA64 |
site_id | AC3 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SAH C 3301 |
Chain | Residue |
C | THR67 |
C | ASP85 |
C | ALA86 |
C | SER87 |
C | MET90 |
C | ALA115 |
C | ASN116 |
C | TRP117 |
C | SER139 |
C | TYR194 |
site_id | AC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SAH D 4301 |
Chain | Residue |
D | ASP85 |
D | ALA86 |
D | SER87 |
D | MET90 |
D | ASN116 |
D | TRP117 |
D | GLY137 |
D | SER139 |
D | HIS142 |
D | HOH4370 |
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 |
A | SER3 | |
D | SER3 | |
D | HIS214 | |
D | ARG239 | |
A | HIS214 | |
A | ARG239 | |
B | SER3 | |
B | HIS214 | |
B | ARG239 | |
C | SER3 | |
C | HIS214 | |
C | ARG239 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:22037183, ECO:0000312|PDB:3THS |
Chain | Residue | Details |
A | TYR5 | |
B | TYR5 | |
C | TYR5 | |
D | TYR5 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0007744|PDB:1NBH |
Chain | Residue | Details |
A | TYR21 | |
B | TYR21 | |
C | TYR21 | |
D | 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 |
A | TRP30 | |
C | ARG40 | |
C | ASP85 | |
C | ASN116 | |
D | TRP30 | |
D | ARG40 | |
D | ASP85 | |
D | ASN116 | |
A | ARG40 | |
A | ASP85 | |
A | ASN116 | |
B | TRP30 | |
B | ARG40 | |
B | ASP85 | |
B | ASN116 | |
C | TRP30 |
site_id | SWS_FT_FI5 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8810903, ECO:0007744|PDB:1XVA |
Chain | Residue | Details |
A | TYR33 | |
D | TYR33 | |
D | LYS175 | |
D | TYR220 | |
A | LYS175 | |
A | TYR220 | |
B | TYR33 | |
B | LYS175 | |
B | TYR220 | |
C | TYR33 | |
C | LYS175 | |
C | 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 |
A | ALA64 | |
B | ALA64 | |
C | ALA64 | |
D | 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 |
A | LEU136 | |
B | LEU136 | |
C | LEU136 | |
D | 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 | |
C | LYS190 | |
C | LYS195 | |
C | LYS200 | |
D | LYS45 | |
D | LYS190 | |
D | LYS195 | |
D | LYS200 | |
A | LYS190 | |
A | LYS195 | |
A | LYS200 | |
B | LYS45 | |
B | LYS190 | |
B | LYS195 | |
B | LYS200 | |
C | LYS45 |
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 | LYS175 | 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 | LYS175 | 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 | LYS175 | 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 | LYS175 | electrostatic stabiliser |
D | TYR194 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |