DB code: D00459

CATH domain 3.40.50.720 : Rossmann fold
3.40.50.720 : Rossmann fold Catalytic domain
E.C. 1.2.1.2
CSA 2nac
M-CSA 2nac
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 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 D00476 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P33160 Formate dehydrogenase
EC 1.2.1.2
NAD-dependent formate dehydrogenase
FDH
PF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
[Graphical View]

KEGG enzyme name
formate dehydrogenase
formate-NAD+ oxidoreductase
FDH I
FDH II
N-FDH
formic hydrogen-lyase
formate hydrogenlyase
hydrogenlyase
NAD+-linked formate dehydrogenase
NAD+-dependent formate dehydrogenase
formate dehydrogenase (NAD+)
NAD+-formate dehydrogenase
formate benzyl-viologen oxidoreductase
formic acid dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P33160 FDH_PSESR Formate + NAD(+) = CO(2) + NADH. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00680 Methane metabolism
MAP00630 Glyoxylate and dicarboxylate metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00058 C00003 C00011 C00004 C00080
E.C.
Compound Formate NAD+ CO2 NADH H+
Type carboxyl group amide group,amine group,nucleotide others amide group,amine group,nucleotide others
ChEBI 30751
15846
16526
16908
15378
PubChem 18971002
284
5893
280
439153
1038
2nacA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2nacB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2nadA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Transition-state-analogue:AZI
2nadB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Transition-state-analogue:AZI
2nacA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2nacB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2nadA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound
2nadB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P33160 & literature [11], [12], [14], [21]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2nacA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2nacB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2nadA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2nadB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2nacA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 146;ARG 284;GLN 313;HIS 332
2nacB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 146;ARG 284;GLN 313;HIS 332
2nadA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 146;ARG 284;GLN 313;HIS 332
2nadB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 146;ARG 284;GLN 313;HIS 332

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[8]
p.451
[11]
[12]
Fig. 2, p.106
[14]
Scheme 1, p.475
[21]
p.148

References
[1]
Resource
Comments
Medline ID
PubMed ID 7144587
Journal Methods Enzymol
Year 1982
Volume 89 Pt D
Pages 531-7
Authors Hopner T, Ruschig U, Muller U, Willnow P
Title Formate dehydrogenase from Pseudomonas oxalaticus.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6311213
Journal Biochem Biophys Res Commun
Year 1983
Volume 115
Pages 61-7
Authors Durfor CN, Wetherbee PJ, Deaton JC, Solomon EI
Title Characterization and spectroscopic properties of reduced Mo and W formate dehydrogenase from C. thermoaceticum.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 6309816
Journal J Biol Chem
Year 1983
Volume 258
Pages 10839-45
Authors Barber MJ, Siegel LM, Schauer NL, May HD, Ferry JG
Title Formate dehydrogenase from Methanobacterium formicicum. Electron paramagnetic resonance spectroscopy of the molybdenum and iron-sulfur centers.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3038082
Journal Biochem J
Year 1987
Volume 243
Pages 235-9
Authors Gadsby PM, Greenwood C, Coddington A, Thomson AJ, Godfrey C
Title Purification and properties of formate dehydrogenase from Pseudomonas aeruginosa. Electron-paramagnetic-resonance studies on the molybdenum centre.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3038081
Journal Biochem J
Year 1987
Volume 243
Pages 225-33
Authors Godfrey C, Coddington A, Greenwood C, Thomson AJ, Gadsby PM
Title Purification and properties of formate dehydrogenase from Pseudomonas aeruginosa. Characterization of haem and iron-sulphur centres by magnetic-circular-dichroism and electron-paramagnetic-resonance spectroscopy.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 3038083
Journal Biochem J
Year 1987
Volume 243
Pages 241-8
Authors Godfrey C, Gadsby PM, Thomson AJ, Greenwood C, Coddington A
Title Electron-paramagnetic-resonance and magnetic-circular-dichroism studies on the formate dehydrogenase-nitrate reductase particle from Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 1657982
Journal J Biol Chem
Year 1991
Volume 266
Pages 21853-63
Authors Jollie DR, Lipscomb JD
Title Formate dehydrogenase from Methylosinus trichosporium OB3b. Purification and spectroscopic characterization of the cofactors.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS)
Medline ID 92283270
PubMed ID 1597184
Journal Eur J Biochem
Year 1992
Volume 206
Pages 441-52
Authors Lamzin VS, Aleshin AE, Strokopytov BV, Yukhnevich MG, Popov VO, Harutyunyan EH, Wilson KS
Title Crystal structure of NAD-dependent formate dehydrogenase.
Related PDB
Related UniProtKB P33160
[9]
Resource
Comments MUTAGENESIS OF CYS-255
Medline ID 93249485
PubMed ID 8484798
Journal Biochem Biophys Res Commun
Year 1993
Volume 192
Pages 976-81
Authors Tishkov VI, Galkin AG, Marchenko GN, Egorova OA, Sheluho DV, Kulakova LB, Dementieva LA, Egorov AM
Title Catalytic properties and stability of a Pseudomonas sp.101 formate dehydrogenase mutants containing Cys-255-Ser and Cys-255-Met replacements.
Related PDB
Related UniProtKB P33160
[10]
Resource
Comments
Medline ID
PubMed ID 8509325
Journal J Bacteriol
Year 1993
Volume 175
Pages 3703-9
Authors Chow CM, RajBhandary UL
Title Developmental regulation of the gene for formate dehydrogenase in Neurospora crassa.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8114093
Journal J Mol Biol
Year 1994
Volume 236
Pages 759-85
Authors Lamzin VS, Dauter Z, Popov VO, Harutyunyan EH, Wilson KS
Title High resolution structures of holo and apo formate dehydrogenase.
Related PDB 2nac 2nad
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8706817
Journal FEBS Lett
Year 1996
Volume 390
Pages 104-8
Authors Tishkov VI, Matorin AD, Rojkova AM, Fedorchuk VV, Savitsky PA, Dementieva LA, Lamzin VS, Mezentzev AV, Popov VO
Title Site-directed mutagenesis of the formate dehydrogenase active centre: role of the His332-Gln313 pair in enzyme catalysis.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9020054
Journal Biochem Biophys Res Commun
Year 1997
Volume 230
Pages 30-4
Authors Duarte RO, Reis AR, Girio F, Moura I, Moura JJ, Collaco TA
Title The formate dehydrogenase isolated from the aerobe Methylobacterium sp. RXM is a molybdenum-containing protein.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9020883
Journal Biochem J
Year 1997
Volume 321
Pages 475-80
Authors Mesentsev AV, Lamzin VS, Tishkov VI, Ustinnikova TB, Popov VO
Title Effect of pH on kinetic parameters of NAD+-dependent formate dehydrogenase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9481877
Journal Biochemistry (Mosc)
Year 1997
Volume 62
Pages 1439-43
Authors Klyachko NL, Vakula SV, Gladyshev VN, Tishkov VI, Levashov AV
Title Formate dehydrogenase in a reversed micelle system: regulation of catalytic activity and oligomeric composition of the enzyme.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10069397
Journal FEBS Lett
Year 1999
Volume 445
Pages 183-8
Authors Rojkova AM, Galkin AG, Kulakova LB, Serov AE, Savitsky PA, Fedorchuk VV, Tishkov VI
Title Bacterial formate dehydrogenase. Increasing the enzyme thermal stability by hydrophobization of alpha-helices.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10691964
Journal Eur J Biochem
Year 2000
Volume 267
Pages 1280-9
Authors Slusarczyk H, Felber S, Kula MR, Pohl M
Title Stabilization of NAD-dependent formate dehydrogenase from Candida boidinii by site-directed mutagenesis of cysteine residues.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11171126
Journal Biochem J
Year 2001
Volume 354
Pages 455-63
Authors Labrou NE, Rigden DJ
Title Active-site characterization of Candida boidinii formate dehydrogenase.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12144528
Journal Biochem J
Year 2002
Volume 367
Pages 841-7
Authors Serov AE, Popova AS, Fedorchuk VV, Tishkov VI
Title Engineering of coenzyme specificity of formate dehydrogenase from Saccharomyces cerevisiae.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12460112
Journal Biochemistry (Mosc)
Year 2002
Volume 67
Pages 1145-51
Authors Fedorchuk VV, Galkin AG, Yasny IE, Kulakova LB, Rojkova AM, Filippova AA, Tishkov VI
Title Effect of interactions between amino acid residues 43 and 61 on thermal stability of bacterial formate dehydrogenases.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11825616
Journal Biochim Biophys Acta
Year 2002
Volume 1594
Pages 136-49
Authors Galkin AG, Kutsenko AS, Bajulina NP, Esipova NG, Lamzin VS, Mesentsev AV, Shelukho DV, Tikhonova TV, Tishkov VI, Ustinnikova TB, Popov VO
Title Site-directed mutagenesis of the essential arginine of the formate dehydrogenase active centre.
Related PDB
Related UniProtKB

Comments

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