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Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 4, component A




Gene: hyfA Accession Numbers: EG11150 (EcoCyc), b2481, ECK2477

Synonyms: yffE

Regulation Summary Diagram

Regulation summary diagram for hyfA

Component of: hydrogenase 4 (extended summary available)

Summary:
This subunit contains four 4Fe-4S clusters and may be involved in electron transfer. [Andrews97] Sequence similarity suggests that it may also contain β-barrel structure(s). [Zhai02]

Locations: membrane

Map Position: [2,599,223 -> 2,599,840] (56.02 centisomes, 202°)
Length: 618 bp / 205 aa

Molecular Weight of Polypeptide: 22.154 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008179, DIP:DIP-9983N, EchoBASE:EB1139, EcoGene:EG11150, EcoliWiki:b2481, ModBase:P23481, OU-Microarray:b2481, PortEco:hyfA, PR:PRO_000022963, Pride:P23481, Protein Model Portal:P23481, RefSeq:NP_416976, RegulonDB:EG11150, SMR:P23481, String:511145.b2481, UniProt:P23481

Relationship Links: InterPro:IN-FAMILY:IPR001450, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, Pfam:IN-FAMILY:PF00037, Pfam:IN-FAMILY:PF12798, Pfam:IN-FAMILY:PF12800, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 223 (21 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for hyfA


GO Terms:
Biological Process:
Inferred by computational analysisGO:0009061 - anaerobic respiration [Gaudet10]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0009055 - electron carrier activity [Gaudet10]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0016020 - membrane [Gaudet10]

MultiFun Terms: metabolismenergy metabolism, carbonanaerobic respiration

Essentiality data for hyfA knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of: hydrogenase 4

Inferred by computational analysis

Synonyms: Hyf, HYD4

Subunit composition of hydrogenase 4 = [HyfG][HyfI][HyfA][HyfB][HyfC][HyfD][HyfE][HyfF][HyfH]
         hydrogenase 4, large subunit = HyfG (summary available)
         hydrogenase 4, small subunit = HyfI (summary available)
         hydrogenase 4, component A = HyfA (summary available)
         hydrogenase 4, component B = HyfB
         hydrogenase 4, component C = HyfC
         hydrogenase 4, component D = HyfD
         hydrogenase 4, component E = HyfE
         hydrogenase 4, component F = HyfF
         hydrogenase 4, component H = HyfH (summary available)

Summary:
On the basis of sequence similarity to hycBCDEFG, which encodes hydrogenase 3, the ten-gene cluster hyfABCDEFGHIJ was presumed to encode a hydrogenase that interacts with formate dehydrogenase (FdhF) to produce an active formate hydrogenlyase complex. The complex cleaves formate to dihydrogen and carbon dioxide [Andrews97]. In support of this presumption, an H+-K+ exchange activity was detected in osmotically stressed cells of wildtype but not in similarly treated cells from an hyf mutant [Bagramyan01]. Further, formate-dependent expression of an hyf-lac fusion was reported to occur with FhlA as an activator [Skibinski02]. However, subsequent experiments indicate that the hyf operon is probably silent in E. coli, at least under the environmental conditions examined, because mutant strains that cannot make hydrogenases 1, 2, and 3 lack hydrogenase activity and fusion strains express significant activity only in the presence of high levels of HyfR [Self04].


Enzymatic reaction of: hydrogenase

2 H+ + 2 e- → H2

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Protein sequence of hydrogenase 4, component A with features indicated

Feature Class Location Citations Comment
Conserved-Region 2 -> 31
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 1.
Metal-Binding-Site 12
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 15
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 18
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 22
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Conserved-Region 41 -> 72
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 2.
Metal-Binding-Site 51
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 54
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 59
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Metal-Binding-Site 63
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Conserved-Region 73 -> 102
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 3.
Metal-Binding-Site 82
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 85
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 88
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 4 (4Fe-4S).
Metal-Binding-Site 92
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 3 (4Fe-4S).
Conserved-Region 140 -> 172
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 4.
Metal-Binding-Site 146
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 149
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 158
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 162
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).


Sequence Pfam Features

Protein sequence of hydrogenase 4, component A with features indicated

Feature Class Location Citations Comment
Pfam PF12800 11 -> 23
Inferred by computational analysis[Finn14]
Fer4_4 : 4Fe-4S binding domain
Pfam PF12798 51 -> 67
Inferred by computational analysis[Finn14]
Fer4_3 : 4Fe-4S binding domain
Pfam PF00037 76 -> 98
Inferred by computational analysis[Finn14]
Fer4 : 4Fe-4S binding domain


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b2481 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11150; confirmed by SwissProt match.


References

Andrews97: Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P, Guest JR (1997). "A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system." Microbiology 1997;143 ( Pt 11);3633-47. PMID: 9387241

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bagramyan01: Bagramyan K, Vassilian A, Mnatsakanyan N, Trchounian A (2001). "Participation of hyf-encoded hydrogenase 4 in molecular hydrogen release coupled with proton-potassium exchange in Escherichia coli." Membr Cell Biol 14(6);749-63. PMID: 11817571

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Self04: Self WT, Hasona A, Shanmugam KT (2004). "Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli." J Bacteriol 186(2);580-7. PMID: 14702328

Skibinski02: Skibinski DA, Golby P, Chang YS, Sargent F, Hoffman R, Harper R, Guest JR, Attwood MM, Berks BC, Andrews SC (2002). "Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR." J Bacteriol 2002;184(23);6642-53. PMID: 12426353

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zhai02: Zhai Y, Saier MH (2002). "The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes." Protein Sci 11(9);2196-207. PMID: 12192075


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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