DB code: D00476

CATH domain 3.40.50.720 : Rossmann fold
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 Catalytic domain
E.C. 1.2.1.59
CSA 1cf2
M-CSA 1cf2
MACiE

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 T00219 D00003 D00010 D00017 D00023 D00027 D00028 D00034

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P10618 Glyceraldehyde-3-phosphate dehydrogenase
GAPDH
EC 1.2.1.59
NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
YP_004003841.1 (Protein)
NC_014658.1 (DNA/RNA sequence)
PF02800 (Gp_dh_C)
PF00044 (Gp_dh_N)
[Graphical View]
P39460 Glyceraldehyde-3-phosphate dehydrogenase
GAPDH
EC 1.2.1.59
NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase
NP_342058.1 (Protein)
NC_002754.1 (DNA/RNA sequence)
PF02800 (Gp_dh_C)
PF00044 (Gp_dh_N)
[Graphical View]

KEGG enzyme name
glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+)(phosphorylating)
triosephosphate dehydrogenase (NAD(P))
glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) (phosphorylating)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P39460 G3P_SULSO D-glyceraldehyde 3-phosphate + phosphate + NAD(P)(+) = 3-phospho-D-glyceroyl phosphate + NAD(P)H. Homotetramer. Cytoplasm.
P10618 G3P_METFE D-glyceraldehyde 3-phosphate + phosphate + NAD(P)(+) = 3-phospho-D-glyceroyl phosphate + NAD(P)H. Homotetramer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00710 Carbon fixation in photosynthetic organisms
MAP00010 Glycolysis / Gluconeogenesis

Compound table
Substrates Products Intermediates
KEGG-id C00118 C00009 C00003 C00006 C00236 C00004 C00005 C00080
E.C.
Compound D-Glyceraldehyde 3-phosphate Orthophosphate NAD+ NADP+ 3-Phospho-D-glyceroyl phosphate NADH NADPH H+
Type carbohydrate,phosphate group/phosphate ion phosphate group/phosphate ion amide group,amine group,nucleotide amide group,amine group,nucleotide carbohydrate,phosphate group/phosphate ion amide group,amine group,nucleotide amide group,amine group,nucleotide others
ChEBI 29052
26078
15846
18009
16001
16908
16474
15378
PubChem 439168
1004
22486802
5893
5886
439191
439153
5884
1038
1b7gO01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b7gQ01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1cf2O01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound
1cf2P01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound
1cf2Q01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound
1cf2R01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound
1b7gO02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4_601 Unbound Unbound Unbound Unbound Unbound
1b7gQ02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4_602 Unbound Unbound Unbound Unbound Unbound
1cf2O02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound Unbound Unbound Unbound
1cf2P02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound Unbound Unbound Unbound
1cf2Q02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound Unbound Unbound Unbound
1cf2R02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1b7g & literature [5], [6] & [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b7gO01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant I2V
1b7gQ01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant I2V
1cf2O01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cf2P01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cf2Q01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1cf2R01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1b7gO02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 139;HIS 219
1b7gQ02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 139;HIS 219
1cf2O02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 140;HIS 219
1cf2P02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 140;HIS 219
1cf2Q02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 140;HIS 219
1cf2R02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 140;HIS 219

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.655-656
[6]
p.495-497
[9]
p.115-117

References
[1]
Resource
Comments
Medline ID
PubMed ID 9761871
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 671-4
Authors Fleming TM, Jones CE, Piper PW, Cowan DA, Isupov MN, Littlechild JA
Title Characterization, crystallization and preliminary X-ray investigation of glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9632884
Journal Biochemistry (Mosc)
Year 1998
Volume 63
Pages 504-15
Authors Nagradova NK, Schmalhausen EV
Title D-Glyceraldehyde-3-phosphate dehydrogenase: structural basis and functional role of the acyl transfer reactions.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10393306
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 1353-5
Authors Charron C, Talfournier F, Isupov MN, Branlant G, Littlechild JA, Vitoux B, Aubry A
Title Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus.
Related PDB 1cf2
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10491162
Journal Eur J Biochem
Year 1999
Volume 265
Pages 93-104
Authors Talfournier F, Colloc'h N, Mornon JP, Branlant G
Title Functional characterization of the phosphorylating D-glyceraldehyde 3-phosphate dehydrogenase from the archaeon Methanothermus fervidus by comparative molecular modelling and site-directed mutagenesis.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS)
Medline ID 99380409
PubMed ID 10448043
Journal J Mol Biol
Year 1999
Volume 291
Pages 651-60
Authors Isupov MN, Fleming TM, Dalby AR, Crowhurst GS, Bourne PC, Littlechild JA
Title Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.
Related PDB 1b7g
Related UniProtKB P39460
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID 20181873
PubMed ID 10715215
Journal J Mol Biol
Year 2000
Volume 297
Pages 481-500
Authors Charron C, Talfournier F, Isupov MN, Littlechild JA, Branlant G, Vitoux B, Aubry A
Title The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP(+) at 2.1 A resolution.
Related PDB
Related UniProtKB P10618
[7]
Resource
Comments
Medline ID
PubMed ID 12369901
Journal Curr Protein Pept Sci
Year 2001
Volume 2
Pages 61-72
Authors Brune B, Mohr S
Title Protein thiol modification of glyceraldehyde-3-phosphate dehydrogenase and caspase-3 by nitric oxide.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11438534
Journal J Biol Chem
Year 2001
Volume 276
Pages 35247-52
Authors Qi J, Isupov MN, Littlechild JA, Anderson LE
Title Chloroplast glyceraldehyde-3-phosphate dehydrogenase contains a single disulfide bond located in the C-terminal extension to the B subunit.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11265453
Journal Methods Enzymol
Year 2001
Volume 331
Pages 105-17
Authors Littlechild JA, Isupov M
Title Glyceraldehyde-3-phosphate dehydrogenase from Sulfolobus solfataricus.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 12382287
Journal Biopolymers
Year 2002
Volume 65
Pages 263-73
Authors Charron C, Vitoux B, Aubry A
Title Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11742130
Journal Protein Sci
Year 2002
Volume 11
Pages 137-46
Authors Orru S, Ruoppolo M, Francese S, Vitagliano L, Marino G, Esposito C
Title Identification of tissue transglutaminase-reactive lysine residues in glyceraldehyde-3-phosphate dehydrogenase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 15046583
Journal Biochem Soc Trans
Year 2004
Volume 32
Pages 255-8
Authors Littlechild JA, Guy JE, Isupov MN
Title Hyperthermophilic dehydrogenase enzymes.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 15048777
Journal Biopolymers
Year 2004
Volume 73
Pages 533-41
Authors Waingeh VF, Lowe SL, Thomasson KA
Title Brownian dynamics of interactions between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mutants and F-actin.
Related PDB
Related UniProtKB

Comments
There are several types of glyceraldehyde-3-phosphate dehydrogenases:
NADP-dependent GAPDH (E.C. 1.2.1.9)
NAD(P)-dependent GAPDH (phosphorylating) (E.C. 1.2.1.59)
GAPDH (phosphorylating) (E.C. 1.2.1.12)
NADP-dependent GAPDH (phosphorylating) (E.C. 1.2.1.13)
This enzyme corresponds to NAD(P)-dependent GAPDH (phosphorylating) (E.C. 1.2.1.59).

Created Updated
2005-01-14 2009-02-26