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O13437

- FDH_CANBO

UniProt

O13437 - FDH_CANBO

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Protein
Formate dehydrogenase
Gene
FDH1, FDH, FDH3
Organism
Candida boidinii (Yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

NAD+-dependent enzyme which catalyzes the final step in the menthanol oxidation pathway. Involved in detoxification of formate.2 Publications

Catalytic activityi

Formate + NAD+ = CO2 + NADH.5 Publications

Enzyme regulationi

Cu2+, Hg and p-chloromercuribenzoate are strong inhibitors of enzyme activity and Ca2+, Mg2+, Zn2+, Mn2+, Cd2+ and Sn2+ have no effect on activity indicating a cysteine residue in the protein is essential for enzyme activity or to maintain the proper structure of the enzyme. Nitrite and nitrate inhibit some enzyme activity, however cyanide, azide, thiocyanate and cyanate are strong inhibitors of the enzymic reaction. The inhibition of cyanide is competitive with formate and reversible.1 Publication

Kineticsi

  1. KM=13 mM for formate (at 30 degrees Celsius and at pH 7.5)5 Publications
  2. KM=0.09 mM for NAD (at 30 degrees Celsius and at pH 7.5)1 Publication
  3. KM=5.6 mM for formate (at 30 degrees Celsius and at pH 7.5)
  4. KM=0.045 mM for NAD (at 30 degrees Celsius and at pH 7.5)1 Publication
  5. KM=2.42 mM for formate (at 25 degrees Celsius and at pH 7.5)
  6. KM=0.04 mM for NAD (at 25 degrees Celsius and at pH 7.5)1 Publication
  7. KM=2.4 mM for formate (at 25 degrees Celsius and at pH 7.6)
  8. KM=0.04 mM for NAD (at 25 degrees Celsius and at pH 7.6)1 Publication
  9. KM=20.0 mM for formate (at 20 degrees Celsius, at pH 7.5 and after 2 weeks of storage at 4 degrees Celsius in GF buffer)
  10. KM=0.05 mM for NAD (at 20 degrees Celsius, at pH 7.5 and after 2 weeks of storage at 4 degrees Celsius in GF buffer)1 Publication
  11. KM=35.0 mM for formate (at 20 degrees Celsius, at pH 7.5 and after 4 months of storage at 4 degrees Celsius in GF buffer)
  12. KM=0.09 mM for NAD (at 20 degrees Celsius, at pH 7.5 and after 4 months of storage at 4 degrees Celsius in GF buffer)1 Publication

Vmax=6 µM/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 7.5-8.5.1 Publication

Temperature dependencei

Broad temperature optima between 45 and 55 degrees Celsius. Reaction rate increases steeply up to 55 degrees Celsius. 50% of activity lost after incubation for 20 minutes at 57 degrees Celsius. Thermal stability increases in the presence of glycerol.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei258 – 2581 By similarityBy similarity
Binding sitei282 – 2821NAD By similarityBy similarity
Active sitei311 – 3111Proton donor By similarityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi159 – 1668ATP Reviewed prediction
Nucleotide bindingi174 – 1752NAD By similarityBy similarity
Nucleotide bindingi256 – 2583NAD By similarityBy similarity
Nucleotide bindingi311 – 3144NAD By similarityBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. NAD+ binding Source: UniProtKB
  3. formate dehydrogenase (NAD+) activity Source: UniProtKB
  4. oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Source: InterPro
  5. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. NADH metabolic process Source: UniProtKB
  2. NADH regeneration Source: UniProtKB
  3. choline catabolic process Source: UniProtKB
  4. formate catabolic process Source: UniProtKB
  5. methanol oxidation Source: UniProtKB
  6. methylamine metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

ATP-binding, NAD, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17206.
SABIO-RKO13437.

Names & Taxonomyi

Protein namesi
Recommended name:
Formate dehydrogenase (EC:1.2.1.2)
Alternative name(s):
NAD-dependent formate dehydrogenase
Gene namesi
Name:FDH1
Synonyms:FDH, FDH3
OrganismiCandida boidinii (Yeast)
Taxonomic identifieri5477 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesmitosporic SaccharomycetalesCandida

Subcellular locationi

Cytoplasm By similarity By similarity

GO - Cellular componenti

  1. cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Biotechnological usei

Ideal catalyst for synthesizing chiral compounds of high enantiomeric purity from prochiral precursors due to a favorable thermodynamic equilibrium, the oxidation of formate to carbon dioxide while also reducing NAD to NADH. However, the necessesity for the presence of large quantities of the enzyme and its rapid inactivation under biotransformation conditions results in higher costs for the biocatalyst industry. In order to make this enzymatic reduction viable and to perform it on a larger scale a more efficient and cost effective process has been established. Site-directed mutagenesis has been effective in stabilizing this commercially important enzyme for its application in the biotransformation of trimethyl pyruvate to L-tert leucine.2 Publications

Disruption phenotypei

Is able to grow on methanol in a batch culture experiment, but its growth is greatly inhibited and a toxic level of formate accumulates in the medium. Formate is not detected in the medium in a methanol-limited chemostat culture but deletion mutant shows only one-fourth of the growth yield of the wild-type.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi23 – 231C → S: Slight increase in substrate affinity for formate but no change in affinity for NAD, 9 degrees Celsius decrease in thermal stability compared to the wild-type, significantly higher stability compared to wild-type under biotransformation conditions, significantly more stable in the presence of CuCl(2); when associated with A-262. Large increase in substrate affinity for formate but no significant change in affinity for NAD, 13 degrees Celsius decrease in thermal stability compared to the wild-type, significantly more stable in the presence of CuCl(2); when associated with V-262. No significant change in affinity for formate or NAD, 5 degrees Celsius decrease in thermal stability compared to the wild-type, significantly higher stability compared to wild-type under biotransformation conditions, and significantly more stable in the presence of CuCl(2). 1 Publication
Mutagenesisi47 – 471K → E: Slight increase in substrate affinity for formate and also affinity for NAD increases by half after 2 weeks. Also after 4 months affinity for formate increases by more than half and affinity for NAD increases by more than half. Retains 84% of residual activity after incubation for 20 minutes at a thermal inactivation temperature of 55 degrees Celsius in samples stored for 2 weeks compared to wild-type which loses 50% of its activity at 55 degrees Celsius. 1 Publication
Mutagenesisi69 – 691F → A: 2-fold decrease in substrate affinity for formate, but no significant change in affinity for NAD. A significant reduction in catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi119 – 1191N → A: 94-fold decrease in substrate affinity for formate and 2700-fold decrease in substrate affinity for NAD. A significant reduction in catalytic activity compared to the wild-type; when associated with A-311. 1 Publication
Mutagenesisi119 – 1191N → H: 80-fold decrease in substrate affinity for formate and a 1250-fold decrease in substrate affinity for NAD. A significant reduction in catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi175 – 1751I → A: 2-fold decrease in substrate affinity for formate and a 12-fold decrease in substrate affinity for NAD. A significant reduction in catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi197 – 1971Q → L: 4-fold decrease in substrate affinity for formate but no significant change in affinity for NAD compared to the wild-type. 1 Publication
Mutagenesisi258 – 2581R → A: No catalytic activity. 1 Publication
Mutagenesisi262 – 2621C → A: Slight increase in substrate affinity for formate but no change in affinity for NAD, 9 degrees Celsius decrease in thermal stability compared to the wild-type, greater stability at a higher pH compared to the wild-type; when associated with S-23. 1 Publication
Mutagenesisi262 – 2621C → V: Large increase in substrate affinity for formate but no significant change in affinity for NAD, 13 degrees Celsius decrease in thermal stability compared to the wild-type; when associated with S-23. Great increase in substrate affinity for formate and NAD and 8 degrees Celsius decrease in thermal stability compared to the wild-type. 1 Publication
Mutagenesisi287 – 2871Q → A: 2-fold decrease in substrate affinity for formate and 3-fold decrease in substrate affinity for NAD compared to the wild-type; when associated with A-311. 1 Publication
Mutagenesisi287 – 2871Q → E: 380-fold decrease in substrate affinity for formate and 3-fold decrease in substrate affinity for NAD compared to the wild-type; when associated with T-288. No significant decrease in substrate affinity for formate but a 4-fold decrease in substrate affinity for NAD and a significant reduction in catalytic activity compared to the wild-type, a more acidic pH is seen than in the wild-type, preventing formate binding by a single ionization of a group compared to that of the wild-type. 1 Publication
Mutagenesisi288 – 2881P → T: 380-fold decrease in substrate affinity for formate and 3-fold decrease in substrate affinity for NAD compared to the wild-type; when associated with E-287. 1 Publication
Mutagenesisi311 – 3111H → A: 2-fold decrease in substrate affinity for formate and 3-fold decrease in substrate affinity for NAD compared to the wild-type; when associated with A-287. 93-fold decrease in substrate affinity for formate and 2700-fold decrease in substrate affinity for NAD, and a significant reduction in catalytic activity compared to the wild-type; when associated with A-119. 1 Publication
Mutagenesisi311 – 3111H → Q: 10-fold decrease in substrate affinity for formate and significant reduction in the catalytic activity compared to the wild-type. 1 Publication
Mutagenesisi328 – 3281K → V: A 75% increase in substrate affinity for formate after 2 weeks and a 50% increase in affinity for NAD. However, after 4 months the affinity for formate increases 7-fold and affinity for NAD increases by 2 thirds. Retains 70% of residual activity after incubation for 20 minutes at a thermal inactivation temperature of 55 degrees Celsius in samples stored for 2 weeks compared to wild-type which loses 50% of its activity at 55 degrees Celsius. 1 Publication
Mutagenesisi360 – 3601K → A: Exhibits no change in substrate affinity for formate, but shows a 4-fold decrease in substrate affinity for NAD implying that L-360 side chain forms strong interactions with the cofactor. A higher reaction rate is observed at an acidic and basic pH values. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 364364Formate dehydrogenase
PRO_0000393949Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi104 – 1041N-linked (GlcNAc...) Reviewed prediction

Keywords - PTMi

Glycoprotein

Proteomic databases

PRIDEiO13437.

Expressioni

Inductioni

Expression is strongly induced by methanol, but is completely repressed in the presence of glucose. However, methanol induced expression is equally strong in cells grown on glucose when formate, methylamine or choline is added. No expression is detected in cells grown on glycerol. When formate, methylamine or choline is added to the culture medium of glycerol- or glucose-grown cells, they exhibit an induction of FDH1 expression.2 Publications

Interactioni

Subunit structurei

Homodimer.2 Publications

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65
Helixi12 – 165
Turni24 – 263
Helixi27 – 293
Helixi31 – 366
Beta strandi40 – 456
Beta strandi49 – 524
Helixi53 – 575
Helixi58 – 603
Beta strandi62 – 665
Helixi76 – 816
Beta strandi87 – 937
Helixi100 – 1067
Beta strandi111 – 1144
Helixi120 – 13516
Helixi138 – 1469
Helixi152 – 1565
Beta strandi166 – 1705
Helixi174 – 18310
Helixi184 – 1863
Beta strandi189 – 1946
Helixi201 – 2066
Beta strandi209 – 2113
Helixi215 – 2206
Beta strandi223 – 2275
Turni233 – 2375
Helixi241 – 2444
Beta strandi251 – 2555
Helixi259 – 2613
Helixi264 – 2729
Beta strandi275 – 2828
Beta strandi285 – 2884
Helixi294 – 2974
Beta strandi306 – 3083
Helixi313 – 3153
Helixi317 – 33519
Helixi343 – 3453
Beta strandi346 – 3494

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FSSX-ray1.70A/B/C/D2-364[»]
2J6IX-ray1.55A/B/C/D2-364[»]
ProteinModelPortaliO13437.
SMRiO13437. Positions 2-353.

Miscellaneous databases

EvolutionaryTraceiO13437.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 119119Catalytic By similarityBy similarity1 Publication
Add
BLAST
Regioni120 – 312193Coenzyme-binding By similarityBy similarity1 Publication
Add
BLAST
Regioni313 – 36452Catalytic By similarityBy similarity1 Publication
Add
BLAST

Sequence similaritiesi

Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. FDH subfamily.By similarity

Family and domain databases

Gene3Di3.40.50.720. 2 hits.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O13437-1 [UniParc]FASTAAdd to Basket

« Hide

MKIVLVLYDA GKHAADEEKL YGCTENKLGI ANWLKDQGHE LITTSDKEGE    50
TSELDKHIPD ADIIITTPFH PAYITKERLD KAKNLKLVVV AGVGSDHIDL 100
DYINQTGKKI SVLEVTGSNV VSVAEHVVMT MLVLVRNFVP AHEQIINHDW 150
EVAAIAKDAY DIEGKTIATI GAGRIGYRVL ERLLPFNPKE LLYYDYQALP 200
KEAEEKVGAR RVENIEELVA QADIVTVNAP LHAGTKGLIN KELLSKFKKG 250
AWLVNTARGA ICVAEDVAAA LESGQLRGYG GDVWFPQPAP KDHPWRDMRN 300
KYGAGNAMTP HYSGTTLDAQ TRYAEGTKNI LESFFTGKFD YRPQDIILLN 350
GEYVTKAYGK HDKK 364
Length:364
Mass (Da):40,370
Last modified:January 1, 1998 - v1
Checksum:i1B30982E0D5B77E8
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti9 – 91D → G in strain: 2.2159.
Natural varianti50 – 512ET → GN in strain: 2.2159 and NCYC 1513.
Natural varianti53 – 531E → V in strain: 2.2159 and NCYC 1513.
Natural varianti56 – 561K → Q in strain: 2.2159 and NCYC 1513.
Natural varianti79 – 791L → I in strain: 2.2159 and NCYC 1513.
Natural varianti84 – 841N → K in strain: 2.2159 and NCYC 1513.
Natural varianti108 – 1081K → R in strain: 2.2159.
Natural varianti145 – 1451I → N in strain: 2.2159.
Natural varianti184 – 1841L → V in strain: 2.2159 and NCYC 1513.
Natural varianti202 – 2021E → D in strain: 2.2159 and NCYC 1513.
Natural varianti308 – 3081M → T in strain: 2.2159.
Natural varianti325 – 3251E → Q in strain: 2.2159 and NCYC 1513.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 235KLYGC → EKLYG AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF004096 Genomic DNA. Translation: AAC49766.1.
AJ245934 Genomic DNA. Translation: CAB54834.1.
AJ011046 Genomic DNA. Translation: CAA09466.2.
DQ458777 Genomic DNA. Translation: ABE69165.2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF004096 Genomic DNA. Translation: AAC49766.1 .
AJ245934 Genomic DNA. Translation: CAB54834.1 .
AJ011046 Genomic DNA. Translation: CAA09466.2 .
DQ458777 Genomic DNA. Translation: ABE69165.2 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2FSS X-ray 1.70 A/B/C/D 2-364 [» ]
2J6I X-ray 1.55 A/B/C/D 2-364 [» ]
ProteinModelPortali O13437.
SMRi O13437. Positions 2-353.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi O13437.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-17206.
SABIO-RK O13437.

Miscellaneous databases

EvolutionaryTracei O13437.

Family and domain databases

Gene3Di 3.40.50.720. 2 hits.
InterProi IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view ]
PROSITEi PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Regulation of the formate dehydrogenase gene, FDH1, in the methylotrophic yeast Candida boidinii and growth characteristics of an FDH1-disrupted strain on methanol, methylamine, and choline."
    Sakai Y., Murdanoto A.P., Konishi T., Iwamatsu A., Kato N.
    J. Bacteriol. 179:4480-4485(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 2-45; 57-76; 87-103; 190-201; 207-236; 242-246; 292-326 AND 329-354, FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, INDUCTION.
    Strain: S2.
  2. "Stabilization of NAD-dependent formate dehydrogenase from Candida boidinii by site-directed mutagenesis of cysteine residues."
    Slusarczyk H., Felber S., Kula M.R., Pohl M.
    Eur. J. Biochem. 267:1280-1289(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 1-15, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, BIOTECHNOLOGY, MUTAGENESIS OF CYS-23 AND CYS-262.
    Strain: ATCC 32195.
  3. "Active-site characterization of Candida boidinii formate dehydrogenase."
    Labrou N.E., Rigden D.J.
    Biochem. J. 354:455-463(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 1-30 AND 132-140, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF PHE-69; ASN-119; ILE-175; GLN-197; ARG-258; GLN-287; PRO-288 AND HIS-311.
    Strain: NCYC 1513.
  4. Zhang G., Yang G., Cao Z., Liu M.
    Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: 2.2159.
  5. "Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis."
    Labrou N.E., Rigden D.J., Clonis Y.D.
    Eur. J. Biochem. 267:6657-6664(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 357-363, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-360.
  6. "Purification and properties of formaldehyde dehydrogenase and formate dehydrogenase from Candida boidinii."
    Schute H., Flossdorf J., Sahm H., Kula M.R.
    Eur. J. Biochem. 62:151-160(1976) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
  7. "Continuous computer controlled production of formate dehydrogenase (FDH) and isolation on a pilot scale."
    Weuster-Botz D., Paschold H., Striegel B., Gieren H., Kula M.R., Wandrey C.
    Chem. Eng. Technol. 17:131-137(1994)
    Cited for: BIOTECHNOLOGY.
  8. "High-resolution structures of formate dehydrogenase from Candida boidinii."
    Schirwitz K., Schmidt A., Lamzin V.S.
    Protein Sci. 16:1146-1156(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT GLU-47 AND (1.55 ANGSTROMS) OF MUTANT VAL-328, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, CATALYTIC AND COENZYME-BINDING REGIONS, MUTAGENESIS OF LYS-47 AND LYS-328.

Entry informationi

Entry nameiFDH_CANBO
AccessioniPrimary (citable) accession number: O13437
Secondary accession number(s): O93968, Q1PAH3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 18, 2010
Last sequence update: January 1, 1998
Last modified: September 3, 2014
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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