Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 4, small subunit

Gene: hyfI Accession Numbers: G7306 (EcoCyc), b2489, ECK2485

Regulation Summary Diagram: ?

Regulation summary diagram for hyfI

Component of: hydrogenase 4 (extended summary available)

This is the smaller of the two catalytic subunits. This subunit contains a 4Fe-4S cluster. [Andrews97]

Map Position: [2,608,728 -> 2,609,486] (56.23 centisomes, 202°)
Length: 759 bp / 252 aa

Molecular Weight of Polypeptide: 28.101 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008198 , EchoBASE:EB3969 , EcoGene:EG14217 , EcoliWiki:b2489 , ModBase:P77668 , OU-Microarray:b2489 , PortEco:hyfI , Pride:P77668 , Protein Model Portal:P77668 , RefSeq:NP_416984 , RegulonDB:G7306 , SMR:P77668 , String:511145.b2489 , UniProt:P77668

Relationship Links: InterPro:IN-FAMILY:IPR006137 , InterPro:IN-FAMILY:IPR006138 , Panther:IN-FAMILY:PTHR11995 , Pfam:IN-FAMILY:PF01058 , Prosite:IN-FAMILY:PS01150

In Paralogous Gene Group: 404 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for hyfI

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008137 - NADH dehydrogenase (ubiquinone) activity Inferred by computational analysis [GOA01a, Andrews97]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0048038 - quinone binding Inferred by computational analysis [GOA01a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for hyfI 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)

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

Protein sequence of hydrogenase 4, small subunit with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 41
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 47
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 111
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 141
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Sequence-Conflict 250 -> 252
[Yamamoto97, UniProt10a]
UniProt: (in Ref. 2);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Yamamoto97: Yamamoto Y, Aiba H, Baba T, Hayashi K, Inada T, Isono K, Itoh T, Kimura S, Kitagawa M, Makino K, Miki T, Mitsuhashi N, Mizobuchi K, Mori H, Nakade S, Nakamura Y, Nashimoto H, Oshima T, Oyama S, Saito N, Sampei G, Satoh Y, Sivasundaram S, Tagami H, Horiuchi T (1997). "Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." DNA Res 4(2);91-113. PMID: 9205837

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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 19.0 on Sun Oct 4, 2015, biocyc13.