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




Gene: hyfB Accession Numbers: EG11282 (EcoCyc), b2482, ECK2478

Synonyms: yffF

Regulation Summary Diagram

Regulation summary diagram for hyfB

Component of: hydrogenase 4 (extended summary available)

Citations: [Andrews97]

Gene Citations: [Andrews97]

Locations: inner membrane

Map Position: [2,599,840 -> 2,601,858] (56.03 centisomes, 202°)
Length: 2019 bp / 672 aa

Molecular Weight of Polypeptide: 72.583 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008181, DIP:DIP-9984N, EchoBASE:EB1259, EcoGene:EG11282, EcoliWiki:b2482, Mint:MINT-1254904, OU-Microarray:b2482, PortEco:hyfB, PR:PRO_000022964, Protein Model Portal:P23482, RefSeq:NP_416977, RegulonDB:EG11282, SMR:P23482, String:511145.b2482, UniProt:P23482

Relationship Links: InterPro:IN-FAMILY:IPR001750, InterPro:IN-FAMILY:IPR003918, Pfam:IN-FAMILY:PF00361, Prints:IN-FAMILY:PR01437

In Paralogous Gene Group: 400 (5 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for hyfB


GO Terms:
Biological Process:
Inferred by computational analysisGO:0042773 - ATP synthesis coupled electron transport [GOA01a]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0008137 - NADH dehydrogenase (ubiquinone) activity [GOA01a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a]

MultiFun Terms: cell structuremembrane
metabolismenergy metabolism, carbonanaerobic respiration

Essentiality data for hyfB 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 B with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 6 -> 26
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 31 -> 51
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 80 -> 100
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 120 -> 140
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 165 -> 185
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 200 -> 220
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 243 -> 263
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 273 -> 293
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 312 -> 332
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 343 -> 363
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 385 -> 405
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 428 -> 448
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 475 -> 495
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 505 -> 525
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 532 -> 552
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 652 -> 672
Inferred by computational analysis[UniProt15]
UniProt: Helical.


Sequence Pfam Features

Protein sequence of hydrogenase 4, component B with features indicated

Feature Class Location Citations Comment
Pfam PF00361 136 -> 425
Inferred by computational analysis[Finn14]
Proton_antipo_M : Proton-conducting membrane transporter


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

Gene local context diagram

Transcription Unit

Transcription-unit diagram

Notes:

History:
1/26/1998 (pkarp) Merged genes G7299/b2482 and EG11282/yffF


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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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

GOA01a: 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

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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


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 Pathway Tools version 19.5 (software by SRI International) on Wed May 4, 2016, biocyc14.