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Protein

Formate dehydrogenase

Gene

FDH1

Organism
Candida boidinii (Yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NAD+-dependent oxidation of formate to carbon dioxide. Formate oxidation is the final step in the methanol oxidation pathway in methylotrophic microorganisms. Has a role in the detoxification of exogenous formate in non-methylotrophic organisms.UniRule annotation2 Publications

Catalytic activityi

Formate + NAD+ = CO2 + NADH.UniRule annotation5 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)1 Publication
  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)1 Publication
  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)1 Publication
  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)1 Publication
  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)1 Publication
  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)1 Publication
  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
  1. Vmax=6 µM/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 7.5-8.5.5 Publications

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.5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei93Substrate; via amide nitrogenUniRule annotation1
Binding sitei119SubstrateUniRule annotation1
Binding sitei195NADUniRule annotation1
Binding sitei256NAD; via carbonyl oxygenUniRule annotation1
Sitei258Important for catalytic activityUniRule annotation1 Publication1
Binding sitei282NADUniRule annotation1
Sitei311Important for catalytic activityUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi174 – 175NADUniRule annotation2
Nucleotide bindingi230 – 234NADUniRule annotation5
Nucleotide bindingi311 – 314NADUniRule annotation4

GO - Molecular functioni

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

GO - Biological processi

  • choline catabolic process Source: UniProtKB
  • formate catabolic process Source: UniProtKB
  • methanol oxidation Source: UniProtKB
  • methylamine metabolic process Source: UniProtKB
  • NADH metabolic process Source: UniProtKB
  • NADH regeneration Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

ATP-binding, NAD, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17206.
BRENDAi1.2.1.2. 1100.
SABIO-RKO13437.

Names & Taxonomyi

Protein namesi
Recommended name:
Formate dehydrogenaseUniRule annotationImported (EC:1.2.1.2UniRule annotation5 Publications)
Short name:
FDHUniRule annotation
Alternative name(s):
NAD-dependent formate dehydrogenaseUniRule annotationImported
Gene namesi
Name:FDH11 PublicationImported
Synonyms:FDHImported, FDH3Imported
OrganismiCandida boidinii (Yeast)
Taxonomic identifieri5477 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesPichiaceaeOgataeaOgataea/Candida clade

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Mutagenesisi23C → 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 Publication1
Mutagenesisi47K → 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 Publication1
Mutagenesisi69F → 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 Publication1
Mutagenesisi119N → 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 Publication1
Mutagenesisi119N → 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 Publication1
Mutagenesisi175I → 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 Publication1
Mutagenesisi197Q → L: 4-fold decrease in substrate affinity for formate but no significant change in affinity for NAD compared to the wild-type. 1 Publication1
Mutagenesisi258R → A: No catalytic activity. 1 Publication1
Mutagenesisi262C → 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 Publication1
Mutagenesisi262C → 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 Publication1
Mutagenesisi287Q → 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 Publication1
Mutagenesisi287Q → 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 Publication1
Mutagenesisi288P → 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 Publication1
Mutagenesisi311H → 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 Publication1
Mutagenesisi311H → Q: 10-fold decrease in substrate affinity for formate and significant reduction in the catalytic activity compared to the wild-type. 1 Publication1
Mutagenesisi328K → 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 Publication1
Mutagenesisi360K → 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 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003939491 – 364Formate dehydrogenaseAdd BLAST364

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.1 Publication

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Structurei

Secondary structure

1364
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi12 – 16Combined sources5
Turni24 – 26Combined sources3
Helixi27 – 29Combined sources3
Helixi31 – 36Combined sources6
Beta strandi40 – 45Combined sources6
Beta strandi49 – 52Combined sources4
Helixi53 – 57Combined sources5
Helixi58 – 60Combined sources3
Beta strandi62 – 66Combined sources5
Helixi76 – 81Combined sources6
Beta strandi87 – 93Combined sources7
Helixi100 – 106Combined sources7
Beta strandi111 – 114Combined sources4
Helixi120 – 135Combined sources16
Helixi138 – 146Combined sources9
Helixi152 – 156Combined sources5
Beta strandi166 – 170Combined sources5
Helixi174 – 183Combined sources10
Helixi184 – 186Combined sources3
Beta strandi189 – 194Combined sources6
Helixi201 – 206Combined sources6
Beta strandi209 – 211Combined sources3
Helixi215 – 220Combined sources6
Beta strandi223 – 227Combined sources5
Turni233 – 237Combined sources5
Helixi241 – 244Combined sources4
Beta strandi251 – 255Combined sources5
Helixi259 – 261Combined sources3
Helixi264 – 272Combined sources9
Beta strandi275 – 282Combined sources8
Beta strandi285 – 288Combined sources4
Helixi294 – 297Combined sources4
Beta strandi306 – 308Combined sources3
Helixi313 – 315Combined sources3
Helixi317 – 335Combined sources19
Helixi343 – 345Combined sources3
Beta strandi346 – 349Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FSSX-ray1.70A/B/C/D2-364[»]
2J6IX-ray1.55A/B/C/D2-364[»]
ProteinModelPortaliO13437.
SMRiO13437.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO13437.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 119CatalyticUniRule annotation1 PublicationAdd BLAST118
Regioni120 – 312Coenzyme-bindingUniRule annotation1 PublicationAdd BLAST193
Regioni313 – 358CatalyticUniRule annotation1 PublicationAdd BLAST46

Sequence similaritiesi

Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. FDH subfamily.UniRule annotation

Family and domain databases

CDDicd05302. FDH. 1 hit.
Gene3Di3.40.50.720. 2 hits.
HAMAPiMF_03210. Formate_dehydrogenase. 1 hit.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR033689. FDH_NAD-dep.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
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

        10         20         30         40         50
MKIVLVLYDA GKHAADEEKL YGCTENKLGI ANWLKDQGHE LITTSDKEGE
60 70 80 90 100
TSELDKHIPD ADIIITTPFH PAYITKERLD KAKNLKLVVV AGVGSDHIDL
110 120 130 140 150
DYINQTGKKI SVLEVTGSNV VSVAEHVVMT MLVLVRNFVP AHEQIINHDW
160 170 180 190 200
EVAAIAKDAY DIEGKTIATI GAGRIGYRVL ERLLPFNPKE LLYYDYQALP
210 220 230 240 250
KEAEEKVGAR RVENIEELVA QADIVTVNAP LHAGTKGLIN KELLSKFKKG
260 270 280 290 300
AWLVNTARGA ICVAEDVAAA LESGQLRGYG GDVWFPQPAP KDHPWRDMRN
310 320 330 340 350
KYGAGNAMTP HYSGTTLDAQ TRYAEGTKNI LESFFTGKFD YRPQDIILLN
360
GEYVTKAYGK HDKK
Length:364
Mass (Da):40,370
Last modified:January 1, 1998 - v1
Checksum:i1B30982E0D5B77E8
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti19 – 23KLYGC → EKLYG AA sequence (PubMed:11171126).Curated5
Sequence conflicti23C → T AA sequence (PubMed:7557425).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti9D → G in strain: 2.2159. CuratedImported1
Natural varianti50 – 51ET → GN in strain: 2.2159 and NCYC 1513. 1 Publication2
Natural varianti53E → V in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti56K → Q in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti79L → I in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti84N → K in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti87L → S in strain ATCC 56294 / CBS 8030 / CCRC 21757 / NRRL Y-17325. 1 Publication1
Natural varianti108K → R in strain: 2.2159. CuratedImported1
Natural varianti145I → N in strain: 2.2159. CuratedImported1
Natural varianti184L → V in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti202E → D in strain: 2.2159 and NCYC 1513. 1 Publication1
Natural varianti308M → T in strain: 2.2159. CuratedImported1
Natural varianti325E → Q in strain: 2.2159 and NCYC 1513. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X81129 Genomic DNA. Translation: CAA57036.1.
AF004096 Genomic DNA. Translation: AAC49766.1.
AJ245934 Genomic DNA. Translation: CAB54834.1.
AJ011046 Genomic DNA. Translation: CAA09466.2.
DQ458777 Genomic DNA. Translation: ABE69165.2.
PIRiJC4252.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X81129 Genomic DNA. Translation: CAA57036.1.
AF004096 Genomic DNA. Translation: AAC49766.1.
AJ245934 Genomic DNA. Translation: CAB54834.1.
AJ011046 Genomic DNA. Translation: CAA09466.2.
DQ458777 Genomic DNA. Translation: ABE69165.2.
PIRiJC4252.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FSSX-ray1.70A/B/C/D2-364[»]
2J6IX-ray1.55A/B/C/D2-364[»]
ProteinModelPortaliO13437.
SMRiO13437.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiO13437.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17206.
BRENDAi1.2.1.2. 1100.
SABIO-RKO13437.

Miscellaneous databases

EvolutionaryTraceiO13437.

Family and domain databases

CDDicd05302. FDH. 1 hit.
Gene3Di3.40.50.720. 2 hits.
HAMAPiMF_03210. Formate_dehydrogenase. 1 hit.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR033689. FDH_NAD-dep.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiFDH_CANBO
AccessioniPrimary (citable) accession number: O13437
Secondary accession number(s): O93968, Q00498, Q1PAH3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 18, 2010
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 86 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.