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P07658

- FDHF_ECOLI

UniProt

P07658 - FDHF_ECOLI

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Protein

Formate dehydrogenase H

Gene
fdhF, b4079, JW4040
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

Formate + NAD+ = CO2 + NADH.3 Publications
Formate + acceptor = CO2 + reduced acceptor.3 Publications

Cofactori

Binds 1 4Fe-4S cluster per subunit.2 Publications
Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.2 Publications

Enzyme regulationi

Inhibited by aerobic conditions.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Iron-sulfur (4Fe-4S)
Metal bindingi10 – 101Iron-sulfur (4Fe-4S)
Metal bindingi11 – 111Iron-sulfur (4Fe-4S)
Metal bindingi15 – 151Iron-sulfur (4Fe-4S)
Metal bindingi42 – 421Iron-sulfur (4Fe-4S)
Active sitei44 – 441Electron donor/acceptor
Binding sitei44 – 441Molybdopterin guanine dinucleotide 2
Active sitei140 – 1401Proton donor/acceptor
Metal bindingi140 – 1401Molybdenum
Sitei141 – 1411Important for catalytic activity
Binding sitei297 – 2971Molybdopterin guanine dinucleotide 2; via amide nitrogen
Binding sitei301 – 3011Molybdopterin guanine dinucleotide 1
Sitei333 – 3331Important for catalytic activity
Binding sitei335 – 3351Molybdopterin guanine dinucleotide 1
Binding sitei445 – 4451Molybdopterin guanine dinucleotide 1
Binding sitei478 – 4781Molybdopterin guanine dinucleotide 1
Binding sitei588 – 5881Molybdopterin guanine dinucleotide 1; via amide nitrogen
Binding sitei654 – 6541Molybdopterin guanine dinucleotide 1
Binding sitei655 – 6551Molybdopterin guanine dinucleotide 2
Binding sitei678 – 6781Molybdopterin guanine dinucleotide 1
Binding sitei679 – 6791Molybdopterin guanine dinucleotide 2

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: EcoCyc
  2. electron carrier activity Source: InterPro
  3. formate dehydrogenase (NAD+) activity Source: UniProtKB-EC
  4. molybdenum ion binding Source: EcoCyc
  5. oxidoreductase activity Source: RefGenome

GO - Biological processi

  1. formate oxidation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, Molybdenum, NAD

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:fdhF
Ordered Locus Names:b4079, JW4040
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10285. fdhF.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: EcoCyc
  2. membrane Source: RefGenome
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 715715Formate dehydrogenase HPRO_0000063221Add
BLAST

Expressioni

Inductioni

By formate. Repressed by oxygen, nitrate, nitrite, and other electron acceptors.2 Publications

Gene expression databases

GenevestigatoriP07658.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

DIPiDIP-9572N.
IntActiP07658. 7 interactions.
STRINGi511145.b4079.

Structurei

Secondary structure

1
715
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76
Beta strandi9 – 113
Beta strandi16 – 227
Beta strandi25 – 317
Turni35 – 395
Helixi43 – 475
Helixi50 – 534
Beta strandi57 – 593
Beta strandi69 – 724
Helixi80 – 9819
Helixi100 – 1023
Beta strandi103 – 1064
Helixi114 – 12613
Helixi137 – 1404
Beta strandi143 – 1453
Helixi148 – 1525
Helixi161 – 1666
Beta strandi168 – 1747
Helixi177 – 1804
Helixi182 – 19312
Beta strandi197 – 2015
Helixi207 – 2104
Beta strandi213 – 2164
Helixi223 – 23614
Helixi242 – 2487
Helixi252 – 2609
Helixi265 – 2673
Helixi268 – 2714
Helixi275 – 28713
Beta strandi288 – 2969
Helixi299 – 3013
Beta strandi302 – 3043
Helixi305 – 31814
Beta strandi322 – 3243
Beta strandi328 – 3325
Helixi338 – 3436
Helixi352 – 3543
Helixi360 – 36910
Helixi383 – 3853
Helixi386 – 3916
Beta strandi397 – 4026
Helixi405 – 4084
Beta strandi409 – 4113
Helixi412 – 42110
Beta strandi422 – 43110
Helixi434 – 4374
Beta strandi440 – 4456
Helixi448 – 4503
Beta strandi453 – 4564
Beta strandi460 – 4656
Beta strandi472 – 4743
Helixi478 – 48811
Helixi498 – 50811
Turni510 – 5145
Helixi517 – 5204
Turni521 – 5233
Beta strandi526 – 5283
Beta strandi541 – 5433
Beta strandi553 – 5564
Beta strandi571 – 5733
Beta strandi575 – 5795
Beta strandi583 – 5853
Helixi592 – 5943
Helixi596 – 5994
Beta strandi607 – 6115
Helixi612 – 6187
Beta strandi625 – 6295
Beta strandi634 – 64512
Beta strandi649 – 6524
Beta strandi657 – 6593
Helixi661 – 6633
Turni671 – 6733
Beta strandi681 – 6877
Helixi691 – 71323

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AA6X-ray2.30A1-715[»]
1FDIX-ray2.90A1-715[»]
1FDOX-ray2.80A1-715[»]
2IV2X-ray2.27X1-715[»]
ProteinModelPortaliP07658.
SMRiP07658. Positions 1-715.

Miscellaneous databases

EvolutionaryTraceiP07658.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 56564Fe-4S Mo/W bis-MGD-typeAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni110 – 1123MGD 1 binding
Regioni173 – 1808MGD 2 binding
Regioni201 – 2044MGD 2 binding
Regioni221 – 2233MGD 2 binding
Regioni402 – 4109MGD 1 binding
Regioni428 – 4292MGD 1 binding
Regioni579 – 5813MGD 1 binding
Regioni581 – 5877MGD 2 binding
Regioni661 – 6622MGD 1 binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0243.
HOGENOMiHOG000031440.
KOiK00123.
OMAiMHIDAFV.
OrthoDBiEOG6CVV7G.
PhylomeDBiP07658.

Family and domain databases

InterProiIPR009010. 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]
PfamiPF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view]
SMARTiSM00926. Molybdop_Fe4S4. 1 hit.
[Graphical view]
SUPFAMiSSF50692. SSF50692. 1 hit.
TIGRFAMsiTIGR01591. Fdh-alpha. 1 hit.
PROSITEiPS51669. 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]

Sequencei

Sequence statusi: Complete.

P07658-1 [UniParc]FASTAAdd to Basket

« Hide

MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD    50
FINDTQILTP RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP 100
DAIQTTGSSR GTGNETNYVM QKFARAVIGT NNVDCCARVU HGPSVAGLHQ 150
SVGNGAMSNA INEIDNTDLV FVFGYNPADS HPIVANHVIN AKRNGAKIIV 200
CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY DKAFVASRTE 250
GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT 300
QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT 350
YPGYQYVKDP ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI 400
MGEDPLQTDA ELSAVRKAFE DLELVIVQDI FMTKTASAAD VILPSTSWGE 450
HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ IISEIATRMG YPMHYNNTQE 500
IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT SYLFKEKFDT 550
PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA 600
LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI 650
YMTYQWWIGA CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID 700
EYNKLKTRLR EAALA 715
Length:715
Mass (Da):79,374
Last modified:February 26, 2008 - v2
Checksum:iC7C86F6F704A142D
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191L → V in AAA23754. 1 Publication

Non-standard residue

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Non-standard residuei140 – 1401Selenocysteine1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M13563 Genomic DNA. Translation: AAA23754.2.
U00006 Genomic DNA. Translation: AAC43173.2.
U00096 Genomic DNA. Translation: AAD13462.1.
AP009048 Genomic DNA. Translation: BAE78081.1.
PIRiA24145. DEECFS.
RefSeqiNP_418503.1. NC_000913.3.
YP_492222.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAD13462; AAD13462; b4079.
BAE78081; BAE78081; BAE78081.
GeneIDi12933956.
948584.
KEGGiecj:Y75_p3966.
eco:b4079.
PATRICi32123709. VBIEscCol129921_4203.

Keywords - Coding sequence diversityi

Selenocysteine

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M13563 Genomic DNA. Translation: AAA23754.2 .
U00006 Genomic DNA. Translation: AAC43173.2 .
U00096 Genomic DNA. Translation: AAD13462.1 .
AP009048 Genomic DNA. Translation: BAE78081.1 .
PIRi A24145. DEECFS.
RefSeqi NP_418503.1. NC_000913.3.
YP_492222.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AA6 X-ray 2.30 A 1-715 [» ]
1FDI X-ray 2.90 A 1-715 [» ]
1FDO X-ray 2.80 A 1-715 [» ]
2IV2 X-ray 2.27 X 1-715 [» ]
ProteinModelPortali P07658.
SMRi P07658. Positions 1-715.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9572N.
IntActi P07658. 7 interactions.
STRINGi 511145.b4079.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAD13462 ; AAD13462 ; b4079 .
BAE78081 ; BAE78081 ; BAE78081 .
GeneIDi 12933956.
948584.
KEGGi ecj:Y75_p3966.
eco:b4079.
PATRICi 32123709. VBIEscCol129921_4203.

Organism-specific databases

EchoBASEi EB0281.
EcoGenei EG10285. fdhF.

Phylogenomic databases

eggNOGi COG0243.
HOGENOMi HOG000031440.
KOi K00123.
OMAi MHIDAFV.
OrthoDBi EOG6CVV7G.
PhylomeDBi P07658.

Enzyme and pathway databases

BioCyci EcoCyc:FORMATEDEHYDROGH-MONOMER.
ECOL316407:JW4040-MONOMER.
MetaCyc:FORMATEDEHYDROGH-MONOMER.

Miscellaneous databases

EvolutionaryTracei P07658.
PROi P07658.

Gene expression databases

Genevestigatori P07658.

Family and domain databases

InterProi IPR009010. 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 ]
Pfami PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view ]
SMARTi SM00926. Molybdop_Fe4S4. 1 hit.
[Graphical view ]
SUPFAMi SSF50692. SSF50692. 1 hit.
TIGRFAMsi TIGR01591. Fdh-alpha. 1 hit.
PROSITEi PS51669. 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 ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiFDHF_ECOLI
AccessioniPrimary (citable) accession number: P07658
Secondary accession number(s): P78137, Q2M6M5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: February 26, 2008
Last modified: July 9, 2014
This is version 156 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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