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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: ?

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]

Map Position: [2,599,223 -> 2,599,840] (56.02 centisomes)
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: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for hyfA knockouts: ?

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

Subunit of: hydrogenase 4

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 reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 2 -> 31
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 12
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 15
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 18
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 22
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 41 -> 72
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 51
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 54
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 59
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 63
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 73 -> 102
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Metal-Binding-Site 82
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 85
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 88
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 92
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 140 -> 172
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 4;
Metal-Binding-Site 146
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 149
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 158
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 162
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

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

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, biocyc13.