6TLK
Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0046294 | biological_process | formaldehyde catabolic process |
| B | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0046294 | biological_process | formaldehyde catabolic process |
| C | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0046294 | biological_process | formaldehyde catabolic process |
| D | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0046294 | biological_process | formaldehyde catabolic process |
| E | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0006730 | biological_process | one-carbon metabolic process |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0046294 | biological_process | formaldehyde catabolic process |
| F | 0004488 | molecular_function | methylenetetrahydrofolate dehydrogenase (NADP+) activity |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0006730 | biological_process | one-carbon metabolic process |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0046294 | biological_process | formaldehyde catabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 33 |
| Details | binding site for residue NAP A 401 |
| Chain | Residue |
| A | ASN97 |
| A | LYS156 |
| A | ALA196 |
| A | GLY197 |
| A | ALA198 |
| A | ILE199 |
| A | LEU201 |
| A | TYR221 |
| A | ASN222 |
| A | LYS256 |
| A | H4M404 |
| A | THR102 |
| A | HOH508 |
| A | HOH548 |
| A | HOH578 |
| A | HOH595 |
| A | HOH598 |
| A | HOH599 |
| A | HOH600 |
| A | HOH601 |
| A | HOH657 |
| A | HOH663 |
| A | ALA127 |
| A | HOH692 |
| A | HOH701 |
| A | HOH706 |
| A | HOH719 |
| A | THR129 |
| A | GLY130 |
| A | PRO131 |
| A | VAL132 |
| A | GLY151 |
| A | ARG152 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 402 |
| Chain | Residue |
| A | ARG167 |
| A | HOH527 |
| A | HOH675 |
| A | HOH756 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 403 |
| Chain | Residue |
| A | PHE85 |
| A | GLY86 |
| A | HOH640 |
| D | LYS153 |
| site_id | AC4 |
| Number of Residues | 23 |
| Details | binding site for residue H4M A 404 |
| Chain | Residue |
| A | SER16 |
| A | PHE18 |
| A | ASP19 |
| A | ASN97 |
| A | GLY98 |
| A | THR235 |
| A | LEU250 |
| A | GLY253 |
| A | GLY254 |
| A | LYS256 |
| A | LEU257 |
| A | NAP401 |
| A | HOH512 |
| A | HOH530 |
| A | HOH577 |
| A | HOH619 |
| A | HOH621 |
| A | HOH663 |
| A | HOH671 |
| A | HOH686 |
| A | HOH733 |
| C | TYR51 |
| C | GOL403 |
| site_id | AC5 |
| Number of Residues | 32 |
| Details | binding site for residue NAP B 401 |
| Chain | Residue |
| B | ASN97 |
| B | THR102 |
| B | ALA127 |
| B | THR129 |
| B | GLY130 |
| B | PRO131 |
| B | VAL132 |
| B | GLY151 |
| B | ARG152 |
| B | LYS156 |
| B | ALA196 |
| B | GLY197 |
| B | ALA198 |
| B | ILE199 |
| B | LEU201 |
| B | TYR221 |
| B | ASN222 |
| B | LYS256 |
| B | H4M402 |
| B | HOH557 |
| B | HOH564 |
| B | HOH590 |
| B | HOH591 |
| B | HOH594 |
| B | HOH602 |
| B | HOH606 |
| B | HOH613 |
| B | HOH619 |
| B | HOH621 |
| B | HOH634 |
| B | HOH645 |
| B | HOH663 |
| site_id | AC6 |
| Number of Residues | 18 |
| Details | binding site for residue H4M B 402 |
| Chain | Residue |
| B | ASN97 |
| B | GLY98 |
| B | THR235 |
| B | LEU250 |
| B | GLY253 |
| B | GLY254 |
| B | LYS256 |
| B | NAP401 |
| B | HOH516 |
| B | HOH573 |
| B | HOH593 |
| B | HOH617 |
| B | HOH621 |
| B | HOH661 |
| B | HOH694 |
| B | SER16 |
| B | PHE18 |
| B | ASP19 |
| site_id | AC7 |
| Number of Residues | 30 |
| Details | binding site for residue NAP C 401 |
| Chain | Residue |
| C | ASN97 |
| C | THR102 |
| C | ALA127 |
| C | THR129 |
| C | GLY130 |
| C | PRO131 |
| C | VAL132 |
| C | GLY151 |
| C | ARG152 |
| C | LYS156 |
| C | ALA196 |
| C | GLY197 |
| C | ALA198 |
| C | ILE199 |
| C | LEU201 |
| C | TYR221 |
| C | ASN222 |
| C | LYS256 |
| C | GOL402 |
| C | HOH505 |
| C | HOH529 |
| C | HOH540 |
| C | HOH563 |
| C | HOH579 |
| C | HOH594 |
| C | HOH604 |
| C | HOH613 |
| C | HOH623 |
| C | HOH624 |
| C | HOH651 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | binding site for residue GOL C 402 |
| Chain | Residue |
| C | PHE18 |
| C | ASP19 |
| C | ASN97 |
| C | GLY98 |
| C | LYS256 |
| C | NAP401 |
| C | HOH566 |
| C | HOH641 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 403 |
| Chain | Residue |
| A | H4M404 |
| A | HOH621 |
| C | TYR51 |
| C | PHE88 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue FMT C 404 |
| Chain | Residue |
| C | GLY68 |
| C | HOH510 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 405 |
| Chain | Residue |
| C | VAL111 |
| C | LYS112 |
| C | GLY116 |
| C | LYS285 |
| site_id | AD3 |
| Number of Residues | 32 |
| Details | binding site for residue NAP D 401 |
| Chain | Residue |
| D | ASN97 |
| D | ALA127 |
| D | THR129 |
| D | GLY130 |
| D | PRO131 |
| D | VAL132 |
| D | GLY151 |
| D | ARG152 |
| D | LYS156 |
| D | ALA196 |
| D | GLY197 |
| D | ALA198 |
| D | ILE199 |
| D | LEU201 |
| D | TYR221 |
| D | ASN222 |
| D | LYS256 |
| D | HOH509 |
| D | HOH510 |
| D | HOH537 |
| D | HOH556 |
| D | HOH557 |
| D | HOH578 |
| D | HOH580 |
| D | HOH584 |
| D | HOH587 |
| D | HOH595 |
| D | HOH631 |
| D | HOH645 |
| D | HOH658 |
| D | HOH688 |
| F | HOH567 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue FMT D 402 |
| Chain | Residue |
| D | ALA113 |
| D | ALA114 |
| D | GLU216 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue CL D 403 |
| Chain | Residue |
| D | HIS30 |
| D | HOH526 |
| E | TYR24 |
| E | HIS30 |
| F | HIS30 |
| F | HOH688 |
| site_id | AD6 |
| Number of Residues | 30 |
| Details | binding site for residue NAP E 401 |
| Chain | Residue |
| E | ASN97 |
| E | THR102 |
| E | ALA127 |
| E | THR129 |
| E | GLY130 |
| E | PRO131 |
| E | VAL132 |
| E | GLY151 |
| E | ARG152 |
| E | LYS156 |
| E | ALA196 |
| E | GLY197 |
| E | ALA198 |
| E | ILE199 |
| E | LEU201 |
| E | TYR221 |
| E | ASN222 |
| E | LYS256 |
| E | HOH503 |
| E | HOH506 |
| E | HOH512 |
| E | HOH537 |
| E | HOH561 |
| E | HOH581 |
| E | HOH584 |
| E | HOH597 |
| E | HOH632 |
| E | HOH649 |
| E | HOH662 |
| E | HOH666 |
| site_id | AD7 |
| Number of Residues | 9 |
| Details | binding site for residue GOL E 402 |
| Chain | Residue |
| E | SER16 |
| E | PHE18 |
| E | ASP19 |
| E | ASN97 |
| E | GLY98 |
| E | LYS256 |
| E | HOH508 |
| E | HOH547 |
| E | HOH682 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue FMT E 403 |
| Chain | Residue |
| B | LYS56 |
| E | VAL37 |
| E | HOH527 |
| E | HOH575 |
| E | HOH685 |
| site_id | AD9 |
| Number of Residues | 7 |
| Details | binding site for residue FMT E 404 |
| Chain | Residue |
| D | GLU185 |
| D | LYS188 |
| E | TYR51 |
| E | ARG53 |
| E | GLY54 |
| E | HOH524 |
| E | HOH673 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue FMT E 405 |
| Chain | Residue |
| E | SER2 |
| E | ASP29 |
| E | HOH522 |
| E | HOH525 |
| E | HOH556 |
| site_id | AE2 |
| Number of Residues | 2 |
| Details | binding site for residue FMT E 406 |
| Chain | Residue |
| E | VAL274 |
| E | HOH616 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue FMT E 407 |
| Chain | Residue |
| E | PHE168 |
| E | GLU278 |
| E | HOH550 |
| site_id | AE4 |
| Number of Residues | 34 |
| Details | binding site for residue NAP F 401 |
| Chain | Residue |
| F | ASN97 |
| F | THR102 |
| F | ALA127 |
| F | THR129 |
| F | GLY130 |
| F | PRO131 |
| F | VAL132 |
| F | GLY151 |
| F | ARG152 |
| F | LYS156 |
| F | ALA196 |
| F | GLY197 |
| F | ALA198 |
| F | ILE199 |
| F | LEU201 |
| F | TYR221 |
| F | ASN222 |
| F | LYS256 |
| F | GOL403 |
| F | HOH518 |
| F | HOH536 |
| F | HOH539 |
| F | HOH547 |
| F | HOH548 |
| F | HOH550 |
| F | HOH557 |
| F | HOH603 |
| F | HOH613 |
| F | HOH616 |
| F | HOH633 |
| F | HOH637 |
| F | HOH652 |
| F | HOH684 |
| F | HOH700 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue MG F 402 |
| Chain | Residue |
| D | ASP180 |
| D | HOH503 |
| D | HOH520 |
| D | HOH586 |
| D | HOH600 |
| D | HOH730 |
| site_id | AE6 |
| Number of Residues | 11 |
| Details | binding site for residue GOL F 403 |
| Chain | Residue |
| F | PHE18 |
| F | ASP19 |
| F | ASN97 |
| F | GLY98 |
| F | LYS256 |
| F | NAP401 |
| F | HOH501 |
| F | HOH524 |
| F | HOH535 |
| F | HOH541 |
| F | HOH582 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue GOL F 404 |
| Chain | Residue |
| F | TYR51 |
| F | HOH567 |
| F | HOH617 |
| site_id | AE8 |
| Number of Residues | 1 |
| Details | binding site for residue GOL F 405 |
| Chain | Residue |
| F | PHE85 |
| site_id | AE9 |
| Number of Residues | 3 |
| Details | binding site for residue FMT F 406 |
| Chain | Residue |
| A | GLU146 |
| F | ASN211 |
| F | HOH505 |
| site_id | AF1 |
| Number of Residues | 1 |
| Details | binding site for residue FMT F 407 |
| Chain | Residue |
| F | LYS237 |
| site_id | AF2 |
| Number of Residues | 2 |
| Details | binding site for residue FMT F 408 |
| Chain | Residue |
| F | LYS166 |
| F | ARG167 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11297742 |
| Chain | Residue | Details |
| E | THR195 | |
| E | LYS256 | |
| F | THR129 | |
| F | ARG152 | |
| F | THR195 | |
| F | LYS256 | |
| A | THR129 | |
| A | ARG152 | |
| A | THR195 | |
| A | LYS256 | |
| B | THR129 | |
| B | ARG152 | |
| B | THR195 | |
| B | LYS256 | |
| C | THR129 | |
| C | ARG152 | |
| C | THR195 | |
| C | LYS256 | |
| D | THR129 | |
| D | ARG152 | |
| D | THR195 | |
| D | LYS256 | |
| E | THR129 | |
| E | ARG152 |
