2G82
High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000166 | molecular_function | nucleotide binding |
A | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
A | 0005737 | cellular_component | cytoplasm |
A | 0006006 | biological_process | glucose metabolic process |
A | 0006096 | biological_process | glycolytic process |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
A | 0050661 | molecular_function | NADP binding |
A | 0051287 | molecular_function | NAD binding |
B | 0000166 | molecular_function | nucleotide binding |
B | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0006006 | biological_process | glucose metabolic process |
B | 0006096 | biological_process | glycolytic process |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
B | 0050661 | molecular_function | NADP binding |
B | 0051287 | molecular_function | NAD binding |
C | 0000166 | molecular_function | nucleotide binding |
C | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0006006 | biological_process | glucose metabolic process |
C | 0006096 | biological_process | glycolytic process |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
C | 0050661 | molecular_function | NADP binding |
C | 0051287 | molecular_function | NAD binding |
D | 0000166 | molecular_function | nucleotide binding |
D | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0006006 | biological_process | glucose metabolic process |
D | 0006096 | biological_process | glycolytic process |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
D | 0050661 | molecular_function | NADP binding |
D | 0051287 | molecular_function | NAD binding |
O | 0000166 | molecular_function | nucleotide binding |
O | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
O | 0005737 | cellular_component | cytoplasm |
O | 0006006 | biological_process | glucose metabolic process |
O | 0006096 | biological_process | glycolytic process |
O | 0016491 | molecular_function | oxidoreductase activity |
O | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
O | 0050661 | molecular_function | NADP binding |
O | 0051287 | molecular_function | NAD binding |
P | 0000166 | molecular_function | nucleotide binding |
P | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
P | 0005737 | cellular_component | cytoplasm |
P | 0006006 | biological_process | glucose metabolic process |
P | 0006096 | biological_process | glycolytic process |
P | 0016491 | molecular_function | oxidoreductase activity |
P | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
P | 0050661 | molecular_function | NADP binding |
P | 0051287 | molecular_function | NAD binding |
Q | 0000166 | molecular_function | nucleotide binding |
Q | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
Q | 0005737 | cellular_component | cytoplasm |
Q | 0006006 | biological_process | glucose metabolic process |
Q | 0006096 | biological_process | glycolytic process |
Q | 0016491 | molecular_function | oxidoreductase activity |
Q | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
Q | 0050661 | molecular_function | NADP binding |
Q | 0051287 | molecular_function | NAD binding |
R | 0000166 | molecular_function | nucleotide binding |
R | 0004365 | molecular_function | glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
R | 0005737 | cellular_component | cytoplasm |
R | 0006006 | biological_process | glucose metabolic process |
R | 0006096 | biological_process | glycolytic process |
R | 0016491 | molecular_function | oxidoreductase activity |
R | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
R | 0050661 | molecular_function | NADP binding |
R | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE NA C 1600 |
Chain | Residue |
C | PGE1700 |
C | HOH1853 |
C | HOH1996 |
Q | HOH3563 |
Q | HOH3699 |
site_id | AC2 |
Number of Residues | 32 |
Details | BINDING SITE FOR RESIDUE NAD O 336 |
Chain | Residue |
O | ILE11 |
O | ASN30 |
O | ASP31 |
O | LEU32 |
O | LYS75 |
O | SER93 |
O | THR94 |
O | GLY95 |
O | PHE97 |
O | THR117 |
O | ALA118 |
O | CSD149 |
O | ASN180 |
O | ASN311 |
O | TYR315 |
O | HOH341 |
O | HOH355 |
O | HOH368 |
O | HOH377 |
O | HOH384 |
O | HOH424 |
O | HOH431 |
O | HOH446 |
O | HOH469 |
O | HOH479 |
O | HOH521 |
R | LEU187 |
R | HOH3525 |
O | ASN6 |
O | GLY7 |
O | GLY9 |
O | ARG10 |
site_id | AC3 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE NAD P 336 |
Chain | Residue |
P | ASN6 |
P | GLY7 |
P | GLY9 |
P | ARG10 |
P | ILE11 |
P | ASN30 |
P | ASP31 |
P | LEU32 |
P | LYS75 |
P | SER93 |
P | THR94 |
P | GLY95 |
P | PHE97 |
P | THR117 |
P | ALA118 |
P | CSD149 |
P | ASN180 |
P | ASN311 |
P | TYR315 |
P | HOH337 |
P | HOH343 |
P | HOH351 |
P | HOH361 |
P | HOH369 |
P | HOH396 |
P | HOH404 |
P | HOH411 |
P | HOH417 |
P | HOH422 |
P | HOH455 |
P | HOH476 |
Q | LEU187 |
Q | HOH3520 |
site_id | AC4 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE NAD Q 336 |
Chain | Residue |
Q | HOH3619 |
Q | HOH3631 |
Q | HOH3667 |
Q | HOH3681 |
Q | HOH3688 |
P | LEU187 |
P | HOH339 |
Q | ASN6 |
Q | GLY7 |
Q | GLY9 |
Q | ARG10 |
Q | ILE11 |
Q | ASN30 |
Q | ASP31 |
Q | LEU32 |
Q | LYS75 |
Q | SER93 |
Q | THR94 |
Q | GLY95 |
Q | PHE97 |
Q | THR117 |
Q | ALA118 |
Q | CSD149 |
Q | ASN180 |
Q | ASN311 |
Q | TYR315 |
Q | HOH3504 |
Q | HOH3508 |
Q | HOH3522 |
Q | HOH3541 |
Q | HOH3554 |
Q | HOH3590 |
Q | HOH3601 |
Q | HOH3603 |
site_id | AC5 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE NAD R 336 |
Chain | Residue |
O | LEU187 |
O | HOH347 |
R | ASN6 |
R | GLY7 |
R | GLY9 |
R | ARG10 |
R | ILE11 |
R | ASN30 |
R | ASP31 |
R | LEU32 |
R | LYS75 |
R | SER93 |
R | THR94 |
R | GLY95 |
R | PHE97 |
R | THR117 |
R | ALA118 |
R | CSD149 |
R | ASN180 |
R | ASN311 |
R | TYR315 |
R | HOH3504 |
R | HOH3505 |
R | HOH3508 |
R | HOH3544 |
R | HOH3548 |
R | HOH3573 |
R | HOH3593 |
R | HOH3599 |
R | HOH3607 |
R | HOH3653 |
R | HOH3666 |
R | HOH3672 |
site_id | AC6 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD A 336 |
Chain | Residue |
A | ASN6 |
A | GLY7 |
A | GLY9 |
A | ARG10 |
A | ILE11 |
A | ASP31 |
A | LEU32 |
A | LYS75 |
A | SER93 |
A | THR94 |
A | GLY95 |
A | PHE97 |
A | THR117 |
A | ALA118 |
A | CSD149 |
A | ASN180 |
A | ASN311 |
A | TYR315 |
A | HOH339 |
A | HOH345 |
A | HOH352 |
A | HOH365 |
A | HOH404 |
A | HOH429 |
A | HOH465 |
A | HOH466 |
A | HOH487 |
A | HOH501 |
A | HOH507 |
D | LEU187 |
D | HOH3519 |
site_id | AC7 |
Number of Residues | 32 |
Details | BINDING SITE FOR RESIDUE NAD B 336 |
Chain | Residue |
B | ASN6 |
B | GLY7 |
B | GLY9 |
B | ARG10 |
B | ILE11 |
B | ASP31 |
B | LEU32 |
B | LYS75 |
B | SER93 |
B | THR94 |
B | GLY95 |
B | PHE97 |
B | THR117 |
B | ALA118 |
B | CSD149 |
B | ASN180 |
B | ASN311 |
B | TYR315 |
B | HOH340 |
B | HOH341 |
B | HOH356 |
B | HOH366 |
B | HOH370 |
B | HOH377 |
B | HOH395 |
B | HOH409 |
B | HOH410 |
B | HOH415 |
B | HOH449 |
B | HOH474 |
C | LEU187 |
C | HOH1824 |
site_id | AC8 |
Number of Residues | 32 |
Details | BINDING SITE FOR RESIDUE NAD C 336 |
Chain | Residue |
B | LEU187 |
B | HOH338 |
C | ASN6 |
C | GLY7 |
C | GLY9 |
C | ARG10 |
C | ILE11 |
C | ASN30 |
C | ASP31 |
C | LEU32 |
C | LYS75 |
C | SER93 |
C | THR94 |
C | GLY95 |
C | PHE97 |
C | THR117 |
C | ALA118 |
C | CSD149 |
C | ASN180 |
C | ASN311 |
C | TYR315 |
C | HOH1802 |
C | HOH1803 |
C | HOH1815 |
C | HOH1833 |
C | HOH1847 |
C | HOH1895 |
C | HOH1917 |
C | HOH1918 |
C | HOH1945 |
C | HOH1961 |
C | HOH1994 |
site_id | AC9 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAD D 336 |
Chain | Residue |
A | LEU187 |
A | HOH346 |
D | ASN6 |
D | GLY7 |
D | GLY9 |
D | ARG10 |
D | ILE11 |
D | ASP31 |
D | LEU32 |
D | LYS75 |
D | SER93 |
D | THR94 |
D | GLY95 |
D | PHE97 |
D | THR117 |
D | ALA118 |
D | CSD149 |
D | ASN180 |
D | ASN311 |
D | TYR315 |
D | HOH3509 |
D | HOH3517 |
D | HOH3530 |
D | HOH3536 |
D | HOH3547 |
D | HOH3564 |
D | HOH3579 |
D | HOH3590 |
D | HOH3595 |
D | HOH3650 |
site_id | BC1 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE PGE C 1700 |
Chain | Residue |
C | ASP65 |
C | NA1600 |
C | HOH1853 |
C | HOH1996 |
C | HOH1998 |
Q | ASP65 |
Q | HOH3563 |
Q | HOH3699 |
Q | HOH3722 |
site_id | BC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IPA C 1800 |
Chain | Residue |
C | HOH1862 |
Q | HOH3736 |
R | GLY222 |
site_id | BC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE IPA Q 1801 |
Chain | Residue |
D | GLY222 |
Q | GLU248 |
Q | HOH3546 |
Q | HOH3736 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL R 3502 |
Chain | Residue |
Q | GLU276 |
Q | LYS294 |
Q | LEU295 |
R | ARG193 |
R | THR206 |
R | HOH3623 |
site_id | BC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE GOL Q 3503 |
Chain | Residue |
Q | ARG193 |
Q | THR206 |
R | GLU276 |
R | LYS294 |
site_id | BC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL D 3504 |
Chain | Residue |
C | GLU276 |
C | LEU295 |
D | ARG193 |
D | THR205 |
D | THR206 |
D | MET227 |
D | HOH3637 |
Functional Information from PROSITE/UniProt
site_id | PS00071 |
Number of Residues | 8 |
Details | GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNsL |
Chain | Residue | Details |
O | ALA147-LEU154 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:8611563 |
Chain | Residue | Details |
O | CSD149 | |
P | CSD149 | |
Q | CSD149 | |
R | CSD149 | |
A | CSD149 | |
B | CSD149 | |
C | CSD149 | |
D | CSD149 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8611563, ECO:0000269|Ref.4 |
Chain | Residue | Details |
O | ARG10 | |
R | ARG10 | |
R | ASP31 | |
R | ASN311 | |
A | ARG10 | |
A | ASP31 | |
A | ASN311 | |
B | ARG10 | |
B | ASP31 | |
B | ASN311 | |
C | ARG10 | |
O | ASP31 | |
C | ASP31 | |
C | ASN311 | |
D | ARG10 | |
D | ASP31 | |
D | ASN311 | |
O | ASN311 | |
P | ARG10 | |
P | ASP31 | |
P | ASN311 | |
Q | ARG10 | |
Q | ASP31 | |
Q | ASN311 |
site_id | SWS_FT_FI3 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000269|Ref.4 |
Chain | Residue | Details |
O | LYS75 | |
R | LYS75 | |
R | THR117 | |
R | ASN180 | |
A | LYS75 | |
A | THR117 | |
A | ASN180 | |
B | LYS75 | |
B | THR117 | |
B | ASN180 | |
C | LYS75 | |
O | THR117 | |
C | THR117 | |
C | ASN180 | |
D | LYS75 | |
D | THR117 | |
D | ASN180 | |
O | ASN180 | |
P | LYS75 | |
P | THR117 | |
P | ASN180 | |
Q | LYS75 | |
Q | THR117 | |
Q | ASN180 |
site_id | SWS_FT_FI4 |
Number of Residues | 40 |
Details | BINDING: BINDING => ECO:0000250|UniProtKB:P00362 |
Chain | Residue | Details |
O | SER148 | |
P | ARG230 | |
Q | SER148 | |
Q | THR179 | |
Q | ARG194 | |
Q | THR207 | |
Q | ARG230 | |
R | SER148 | |
R | THR179 | |
R | ARG194 | |
R | THR207 | |
O | THR179 | |
R | ARG230 | |
A | SER148 | |
A | THR179 | |
A | ARG194 | |
A | THR207 | |
A | ARG230 | |
B | SER148 | |
B | THR179 | |
B | ARG194 | |
B | THR207 | |
O | ARG194 | |
B | ARG230 | |
C | SER148 | |
C | THR179 | |
C | ARG194 | |
C | THR207 | |
C | ARG230 | |
D | SER148 | |
D | THR179 | |
D | ARG194 | |
D | THR207 | |
O | THR207 | |
D | ARG230 | |
O | ARG230 | |
P | SER148 | |
P | THR179 | |
P | ARG194 | |
P | THR207 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | SITE: Activates thiol group during catalysis => ECO:0000305|PubMed:8611563 |
Chain | Residue | Details |
O | HIS176 | |
P | HIS176 | |
Q | HIS176 | |
R | HIS176 | |
A | HIS176 | |
B | HIS176 | |
C | HIS176 | |
D | HIS176 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
O | HIS176 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
P | HIS176 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
Q | HIS176 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
R | HIS176 |
site_id | CSA5 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
A | HIS176 |
site_id | CSA6 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
B | HIS176 |
site_id | CSA7 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
C | HIS176 |
site_id | CSA8 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1szj |
Chain | Residue | Details |
D | HIS176 |