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P07658

- FDHF_ECOLI

UniProt

P07658 - FDHF_ECOLI

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Protein

Formate dehydrogenase H

Gene

fdhF

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.
Formate + acceptor = CO2 + reduced acceptor.

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Inhibited by aerobic conditions.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Iron-sulfur (4Fe-4S)2 PublicationsPROSITE-ProRule annotation
Metal bindingi10 – 101Iron-sulfur (4Fe-4S)2 PublicationsPROSITE-ProRule annotation
Metal bindingi11 – 111Iron-sulfur (4Fe-4S)2 PublicationsPROSITE-ProRule annotation
Metal bindingi15 – 151Iron-sulfur (4Fe-4S)2 PublicationsPROSITE-ProRule annotation
Metal bindingi42 – 421Iron-sulfur (4Fe-4S)2 PublicationsPROSITE-ProRule annotation
Active sitei44 – 441Electron donor/acceptor
Binding sitei44 – 441Molybdopterin guanine dinucleotide 22 Publications
Active sitei140 – 1401Proton donor/acceptor
Metal bindingi140 – 1401Molybdenum
Sitei141 – 1411Important for catalytic activity
Binding sitei297 – 2971Molybdopterin guanine dinucleotide 2; via amide nitrogen2 Publications
Binding sitei301 – 3011Molybdopterin guanine dinucleotide 12 Publications
Sitei333 – 3331Important for catalytic activity
Binding sitei335 – 3351Molybdopterin guanine dinucleotide 12 Publications
Binding sitei445 – 4451Molybdopterin guanine dinucleotide 12 Publications
Binding sitei478 – 4781Molybdopterin guanine dinucleotide 12 Publications
Binding sitei588 – 5881Molybdopterin guanine dinucleotide 1; via amide nitrogen2 Publications
Binding sitei654 – 6541Molybdopterin guanine dinucleotide 12 Publications
Binding sitei655 – 6551Molybdopterin guanine dinucleotide 22 Publications
Binding sitei678 – 6781Molybdopterin guanine dinucleotide 12 Publications
Binding sitei679 – 6791Molybdopterin guanine dinucleotide 22 Publications

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.

Gene expression databases

GenevestigatoriP07658.

Interactioni

Subunit structurei

Consists of two separable enzymatic activities: a formate dehydrogenase component (FDH-H) and hydrogenase-3.2 Publications

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07658.

Family & Domainsi

Domains and Repeats

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

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

Phylogenomic databases

eggNOGiCOG0243.
HOGENOMiHOG000031440.
InParanoidiP07658.
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

        10         20         30         40         50
MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD
60 70 80 90 100
FINDTQILTP RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP
110 120 130 140 150
DAIQTTGSSR GTGNETNYVM QKFARAVIGT NNVDCCARVU HGPSVAGLHQ
160 170 180 190 200
SVGNGAMSNA INEIDNTDLV FVFGYNPADS HPIVANHVIN AKRNGAKIIV
210 220 230 240 250
CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY DKAFVASRTE
260 270 280 290 300
GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT
310 320 330 340 350
QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT
360 370 380 390 400
YPGYQYVKDP ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI
410 420 430 440 450
MGEDPLQTDA ELSAVRKAFE DLELVIVQDI FMTKTASAAD VILPSTSWGE
460 470 480 490 500
HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ IISEIATRMG YPMHYNNTQE
510 520 530 540 550
IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT SYLFKEKFDT
560 570 580 590 600
PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA
610 620 630 640 650
LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI
660 670 680 690 700
YMTYQWWIGA CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID
710
EYNKLKTRLR EAALA
Length:715
Mass (Da):79,374
Last modified:February 26, 2008 - v2
Checksum:iC7C86F6F704A142D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191L → V in AAA23754. (PubMed:2941757)Curated

Non-standard residue

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi P07658.
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: November 26, 2014
This is version 159 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