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P07658 (FDHF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 153. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Formate dehydrogenase H

EC=1.1.99.33
EC=1.2.1.2
Alternative name(s):
Formate dehydrogenase-H subunit alpha
Short name=FDH-H
Formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide
Gene names
Name:fdhF
Ordered Locus Names:b4079, JW4040
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length715 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors.

Catalytic activity

Formate + NAD+ = CO2 + NADH. Ref.7 Ref.8 Ref.9

Formate + acceptor = CO2 + reduced acceptor. Ref.7 Ref.8 Ref.9

Cofactor

Binds 1 4Fe-4S cluster per subunit. Ref.7 Ref.8

Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit. Ref.7 Ref.8

Enzyme regulation

Inhibited by aerobic conditions. Ref.6 Ref.7

Subunit structure

Consists of two separable enzymatic activities: a formate dehydrogenase component (FDH-H) and hydrogenase-3.

Induction

By formate. Repressed by oxygen, nitrate, nitrite, and other electron acceptors. Ref.6 Ref.7

Sequence similarities

Belongs to the prokaryotic molybdopterin-containing oxidoreductase family.

Contains 1 4Fe-4S Mo/W bis-MGD-type domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 715715Formate dehydrogenase H
PRO_0000063221

Regions

Domain1 – 56564Fe-4S Mo/W bis-MGD-type
Region110 – 1123MGD 1 binding
Region173 – 1808MGD 2 binding
Region201 – 2044MGD 2 binding
Region221 – 2233MGD 2 binding
Region402 – 4109MGD 1 binding
Region428 – 4292MGD 1 binding
Region579 – 5813MGD 1 binding
Region581 – 5877MGD 2 binding
Region661 – 6622MGD 1 binding

Sites

Active site441Electron donor/acceptor
Active site1401Proton donor/acceptor
Metal binding81Iron-sulfur (4Fe-4S)
Metal binding101Iron-sulfur (4Fe-4S)
Metal binding111Iron-sulfur (4Fe-4S)
Metal binding151Iron-sulfur (4Fe-4S)
Metal binding421Iron-sulfur (4Fe-4S)
Metal binding1401Molybdenum
Binding site441MGD 2
Binding site2971MGD 2; via amide nitrogen
Binding site3011MGD 1
Binding site3351MGD 1
Binding site4451MGD 1
Binding site4781MGD 1
Binding site5881MGD 1; via amide nitrogen
Binding site6541MGD 1
Binding site6551MGD 2
Binding site6781MGD 1
Binding site6791MGD 2
Site1411Important for catalytic activity
Site3331Important for catalytic activity

Amino acid modifications

Non-standard residue1401Selenocysteine Ref.8

Experimental info

Sequence conflict191L → V in AAA23754. Ref.1

Secondary structure

.......................................................................................................................................... 715
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P07658 [UniParc].

Last modified February 26, 2008. Version 2.
Checksum: C7C86F6F704A142D

FASTA71579,374
        10         20         30         40         50         60 
MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD FINDTQILTP 

        70         80         90        100        110        120 
RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP DAIQTTGSSR GTGNETNYVM 

       130        140        150        160        170        180 
QKFARAVIGT NNVDCCARVU HGPSVAGLHQ SVGNGAMSNA INEIDNTDLV FVFGYNPADS 

       190        200        210        220        230        240 
HPIVANHVIN AKRNGAKIIV CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY 

       250        260        270        280        290        300 
DKAFVASRTE GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT 

       310        320        330        340        350        360 
QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT YPGYQYVKDP 

       370        380        390        400        410        420 
ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI MGEDPLQTDA ELSAVRKAFE 

       430        440        450        460        470        480 
DLELVIVQDI FMTKTASAAD VILPSTSWGE HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ 

       490        500        510        520        530        540 
IISEIATRMG YPMHYNNTQE IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT 

       550        560        570        580        590        600 
SYLFKEKFDT PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA 

       610        620        630        640        650        660 
LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI YMTYQWWIGA 

       670        680        690        700        710 
CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID EYNKLKTRLR EAALA 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli."
Zinoni F., Birkmann A., Stadtman T.C., Boeck A.
Proc. Natl. Acad. Sci. U.S.A. 83:4650-4654(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes."
Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.
Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component."
Axley M.J., Grahame D.A., Stadtman T.C.
J. Biol. Chem. 265:18213-18218(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-12, CHARACTERIZATION.
[6]"Characterization of crystalline formate dehydrogenase H from Escherichia coli. Stabilization, EPR spectroscopy, and preliminary crystallographic analysis."
Gladyshev V.N., Boyington J.C., Khangulov S.V., Grahame D.A., Stadtman T.C., Sun P.D.
J. Biol. Chem. 271:8095-8100(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION, CRYSTALLIZATION.
[7]"Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer."
Khangulov S.V., Gladyshev V.N., Dismukes G.C., Stadtman T.C.
Biochemistry 37:3518-3528(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, COFACTOR.
[8]"Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster."
Boyington J.C., Gladyshev V.N., Khangulov S.V., Stadtman T.C., Sun P.D.
Science 275:1305-1308(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (4FE-4S); MOLYBDENUM ION AND MOLYBDOPTERIN, SELENOCYSTEINE AT SEC-140, COFACTOR, CATALYTIC ACTIVITY.
[9]"Formate-reduced E. coli formate dehydrogenase H: The reinterpretation of the crystal structure suggests a new reaction mechanism."
Raaijmakers H.C., Romao M.J.
J. Biol. Inorg. Chem. 11:849-854(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (4FE-4S) AND MOLYBDOPTERIN, CATALYTIC ACTIVITY.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M13563 Genomic DNA. Translation: AAA23754.2.
U00006 Genomic DNA. Translation: AAC43173.2.
U00096 Genomic DNA. Translation: AAD13462.1.
AP009048 Genomic DNA. Translation: BAE78081.1.
PIRDEECFS. A24145.
RefSeqNP_418503.1. NC_000913.3.
YP_492222.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AA6X-ray2.30A1-715[»]
1FDIX-ray2.90A1-715[»]
1FDOX-ray2.80A1-715[»]
2IV2X-ray2.27X1-715[»]
ProteinModelPortalP07658.
SMRP07658. Positions 1-715.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9572N.
IntActP07658. 7 interactions.
STRING511145.b4079.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAD13462; AAD13462; b4079.
BAE78081; BAE78081; BAE78081.
GeneID12933956.
948584.
KEGGecj:Y75_p3966.
eco:b4079.
PATRIC32123709. VBIEscCol129921_4203.

Organism-specific databases

EchoBASEEB0281.
EcoGeneEG10285. fdhF.

Phylogenomic databases

eggNOGCOG0243.
HOGENOMHOG000031440.
KOK00123.
OMANMFEAAL.
OrthoDBEOG6CVV7G.
ProtClustDBCLSK880842.

Enzyme and pathway databases

BioCycEcoCyc:FORMATEDEHYDROGH-MONOMER.
ECOL316407:JW4040-MONOMER.
MetaCyc:FORMATEDEHYDROGH-MONOMER.

Gene expression databases

GenevestigatorP07658.

Family and domain databases

InterProIPR009010. Asp_de-COase-like_dom.
IPR006478. Formate_DH_asu.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
IPR006655. Mopterin_OxRdtase_prok_CS.
IPR027467. MopterinOxRdtase_cofactor_BS.
[Graphical view]
PfamPF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view]
SMARTSM00926. Molybdop_Fe4S4. 1 hit.
[Graphical view]
SUPFAMSSF50692. SSF50692. 1 hit.
TIGRFAMsTIGR01591. Fdh-alpha. 1 hit.
PROSITEPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS00490. MOLYBDOPTERIN_PROK_2. 1 hit.
PS00932. MOLYBDOPTERIN_PROK_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP07658.
PROP07658.

Entry information

Entry nameFDHF_ECOLI
AccessionPrimary (citable) accession number: P07658
Secondary accession number(s): P78137, Q2M6M5
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: February 26, 2008
Last modified: April 16, 2014
This is version 153 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene