Formate dehydrogenase subunit alpha precursor

Names and origin

Protein names

Recommended name:
    Formate dehydrogenase subunit alpha
      Short name=FDH subunit alpha
    EC=1.2.1.2
Alternative name(s):
    Formate dehydrogenase large subunit

Gene names

Name:

fdhA

Organism

Desulfovibrio gigas

Taxonomic identifier

879 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

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Protein attributes

Sequence length	1012 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Alpha chain of the formate dehydrogenase (FDH) catalyze the reversible two-electron oxidation of formate to carbon dioxide. FDH loses activity in the presence of air, but this activity can be restored. The alpha subunit of formate dehydrogenase forms the active site.
Catalytic activity	Formate + NAD⁺ = CO₂ + NADH.
Cofactor	Binds 1 4Fe-4S cluster per subunit. Ref.1 Ref.4 Binds 2 molybdopterin guanine dinucleotide (MGD) groups. Ref.1 Ref.4 Binds 1 tungsten ion per subunit. Ref.1 Ref.4
Subunit structure	Heterodimer of alpha (fdhA) and beta (fdhB) subunits. Ref.1 Ref.4 Ref.3
Subcellular location	Periplasm.
Post-translational modification	The disulfide bond is likely to be broken in the active form of this enzyme. Ref.1 Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.
Sequence similarities	Belongs to the prokaryotic molybdopterin-containing oxidoreductase family.
Biophysicochemical properties	pH dependence: Optimum pH is 7.5-8.0. Temperature dependence: Optimum temperature is 56 degrees Celsius.

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Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Periplasm
Coding sequence diversity	Selenocysteine
Domain	Signal
Ligand	4Fe-4S Calcium Iron Iron-sulfur Metal-binding Molybdenum NAD Selenium Tungsten
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	3D-structure
Gene Ontology (GO)
Biological process	cellular respiration Inferred from electronic annotation. Source: InterPro electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: InterPro periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: InterPro formate dehydrogenase activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW molybdenum ion binding Inferred from electronic annotation. Source: UniProtKB-KW selenium binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 35

35

Tat-type signal Ref.1

Chain

36 – 1012

977

Formate dehydrogenase subunit alpha Ref.1

PRO_0000019149

Regions

Calcium binding

394 – 398

5

Ref.1

Sites

Metal binding

52

1

Iron-sulfur (4Fe-4S) Ref.1

Metal binding

55

1

Iron-sulfur (4Fe-4S) Ref.1

Metal binding

59

1

Iron-sulfur (4Fe-4S) Ref.1

Metal binding

89

1

Iron-sulfur (4Fe-4S) Ref.1

Metal binding

193

1

Tungsten Ref.1

Amino acid modifications

Non-standard residue

193

1

Selenocysteine

Disulfide bond

852 ↔ 879

Ref.1

Secondary structure

1

.

1012

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q934F5-1 [UniParc].

Last modified February 26, 2008. Version 2.
Checksum: 23CDC4594334D51F
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FASTA

1,012

113,271

        10         20         30         40         50         60 
MLIKRRAFLK LTAAGATLSA FGGLGVDLAP AKAQAATMAL KTVDAKQTTS VCCYCSVGCG 

        70         80         90        100        110        120 
LIVHTDKKTN RAINVEGDPD HPINEGSLCA KGASTWQLAE NERRPANPLY RAPGSDQWEE 

       130        140        150        160        170        180 
KSWDWMLDTI AERVAKTREA TFVTKNAKGQ VVNRCDGIAS VGSAAMDNEE CWIYQAWLRS 

       190        200        210        220        230        240 
LGLFYIEHQA RIUHSATVAA LAESYGRGAM TNHWIDLKNS DVILMMGSNP AENHPISFKW 

       250        260        270        280        290        300 
VMRAKDKGAT LIHVDPRYTR TSTKCDLYAP LRSGSDIAFL NGMTKYILEK ELYFKDYVVN 

       310        320        330        340        350        360 
YTNASFIVGE GFAFEEGLFA GYNKETRKYD KSKWGFERDE NGNPKRDETL KHPRCVFQIM 

       370        380        390        400        410        420 
KKHYERYDLD KISAICGTPK ELILKVYDAY CATGKPDKAG TIMYAMGWTQ HTVGVQNIRA 

       430        440        450        460        470        480 
MSINQLLLGN IGVAGGGVNA LRGEANVQGS TDHGLLMHIY PGYLGTARAS IPTYEEYTKK 

       490        500        510        520        530        540 
FTPVSKDPQS ANWWSNFPKY SASYIKSMWP DADLNEAYGY LPKGEDGKDY SWLTLFDDMF 

       550        560        570        580        590        600 
QGKIKGFFAW GQNPACSGAN SNKTREALTK LDWMVNVNIF DNETGSFWRG PDMDPKKIKT 

       610        620        630        640        650        660 
EVFFLPCAVA IEKEGSISNS GRWMQWRYVG PEPRKNAIPD GDLIVELAKR VQKLLAKTPG 

       670        680        690        700        710        720 
KLAAPVTKLK TDYWVNDHGH FDPHKIAKLI NGFALKDFKV GDVEYKAGQQ IATFGHLQAD 

       730        740        750        760        770        780 
GSTTSGCWIY TGSYTEKGNM AARRDKTQTD MQAKIGLYPG WTWAWPVNRR IIYNRASVDL 

       790        800        810        820        830        840 
NGKPYAPEKA VVEWNAAEKK WVGDVPDGPW PPQADKEKGK RAFIMKPEGY AYLYGPGRED 

       850        860        870        880        890        900 
GPLPEYYEPM ECPVIEHPFS KTLHNPTALH FATEEKAVCD PRYPFICSTY RVTEHWQTGL 

       910        920        930        940        950        960 
MTRNTPWLLE AEPQMFCEMS EELATLRGIK NGDKVILESV RGKLWAKAII TKRIKPFAIQ 

       970        980        990       1000       1010 
GQQVHMVGIP WHYGWSFPKN GGDAANILTP SVGDPNTGIP ETKAFMVNVT KA

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References

[1]	"Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas." Raaijmakers H., Macieira S.I.M.G., Dias J.M., Teixeira S., Bursakov S., Huber R., Moura J.J.G., Moura I., Romao M.J. Structure 10:1261-1272(2002) [PubMed: 12220497] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBUNIT, COFACTOR, DISULFIDE BOND, CALCIUM-BINDING, METAL-BINDING, X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH FDHB. Strain: ATCC 19364 / DSM 1382 / NCIB 9332 / VKM B-1759.
[2]	"Properties of formate dehydrogenase from Desulfivibrio gigas." Riederer-Henderson M.A., Peck H.D. Jr. Can. J. Microbiol. 32:430-435(1986) Cited for: CHARACTERIZATION.
[3]	"Purification and characterization of a tungsten-containing formate dehydrogenase from Desulfovibrio gigas." Almendra M.J., Brondino C.D., Gavel O., Pereira A.S., Tavares P., Bursakov S., Duarte R., Caldeira J., Moura J.J.G., Moura I. Biochemistry 38:16366-16372(1999) [PubMed: 10587462] [Abstract] Cited for: CHARACTERIZATION, SUBUNIT. Strain: ATCC 19364 / DSM 1382 / NCIB 9332 / VKM B-1759.
[4]	"Tungsten-containing formate dehydrogenase from Desulfovibrio gigas: metal identification and preliminary structural data by multi-wavelength crystallography." Raaijmakers H., Teixeira S., Dias J.M., Almendra M.J., Brondino C.D., Moura I., Moura J.J.G., Romao M.J. J. Biol. Inorg. Chem. 6:398-404(2001) [PubMed: 11372198] [Abstract] Cited for: COFACTOR, SUBUNIT.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ318781 Genomic DNA. Translation: CAC86667.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H0H	X-ray	1.80	A/K	36-1012	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.2.1.2. 7582.
1.2.2.1. 7582.

Family and domain databases

InterPro

IPR009010. Asp_de-COase-like_fold.
IPR006443. Formate_DH_asu_anaerob.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_Fe4S4_dom.
IPR006655. Mopterin_OxRdtase_prok_CS.
IPR006311. TAT_signal.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

Gene3D

G3DSA:2.40.40.20. Asp_decarboxylase-like_fold. 1 hit.

Pfam

PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01553. formate-DH-alph. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS00490. MOLYBDOPTERIN_PROK_2. False negative.
PS00932. MOLYBDOPTERIN_PROK_3. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

FDHA_DESGI

Accession

Primary (citable) accession number: Q934F5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	February 26, 2008
Last modified:	February 9, 2010
This is version 56 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families