Escherichia coli K-12 substr. MG1655 Polypeptide: protein involved with the maturation of hydrogenases 1 and 2

Gene: hybF Accession Numbers: EG11804 (EcoCyc), b2991, ECK2985

Regulation Summary Diagram: ?

Regulation summary diagram for hybF

HybF and its homolog, HypA, are involved in the maturation of hydrogenase isozymes. HybF is required for maturation of hydrogenase isozymes 1 and 2, while HypA is involved in the maturation of hydrogenase 3; HypA and HybF can only partially substitute for each other [Hube02]. The presence of high levels of nickel can phenotypically rescue hypA and hybF mutants and a triple hypA hypB hybF mutant to a low level [Hube02, Blokesch04a].

Purified HybF contains Zn2+ in stoichiometric amounts. However, C89 in the C-terminal zinc finger motif is not essential for function of HybF. The protein is able to bind Ni2+ in vitro with a KD of 1.87 µM; a H2Q mutation drastically reduces Ni2+ binding. The H2 and E3 residues are also required for the hydrogenase maturation activity of HybF [Blokesch04a].

Review: [Forzi07]

Gene Citations: [Sargent98, Menon94]

Locations: cytosol

Map Position: [3,137,999 <- 3,138,340] (67.63 centisomes, 243°)
Length: 342 bp / 113 aa

Molecular Weight of Polypeptide: 12.697 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009818 , CGSC:33427 , EchoBASE:EB1752 , EcoGene:EG11804 , EcoliWiki:b2991 , OU-Microarray:b2991 , PortEco:hybF , Pride:P0A703 , Protein Model Portal:P0A703 , RefSeq:NP_417465 , RegulonDB:EG11804 , SMR:P0A703 , String:511145.b2991 , UniProt:P0A703

Relationship Links: InterPro:IN-FAMILY:IPR000688 , InterPro:IN-FAMILY:IPR020538 , Pfam:IN-FAMILY:PF01155 , Prosite:IN-FAMILY:PS01249

Genetic Regulation Schematic: ?

Genetic regulation schematic for hybF

GO Terms:

Biological Process: GO:0051604 - protein maturation Inferred from experiment [Hube02]
GO:0006464 - cellular protein modification process Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Blokesch04a]
GO:0016151 - nickel cation binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Blokesch04a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer protein related posttranslational modification
metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for hybF 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]

Last-Curated ? 21-Mar-2012 by Keseler I , SRI International

Sequence Features

Protein sequence of protein involved with the maturation of hydrogenases 1 and 2 with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 2
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 73
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 76
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 89
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 92
UniProt: Nickel; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2991 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11804; confirmed by SwissProt match.


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

Blokesch04a: Blokesch M, Rohrmoser M, Rode S, Bock A (2004). "HybF, a zinc-containing protein involved in NiFe hydrogenase maturation." J Bacteriol 186(9);2603-11. PMID: 15090500

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

Forzi07: Forzi L, Sawers RG (2007). "Maturation of [NiFe]-hydrogenases in Escherichia coli." Biometals 20(3-4):565-78. PMID: 17216401

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hube02: Hube M, Blokesch M, Bock A (2002). "Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF." J Bacteriol 184(14);3879-85. PMID: 12081959

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

Menon94: Menon NK, Chatelus CY, Dervartanian M, Wendt JC, Shanmugam KT, Peck HD, Przybyla AE (1994). "Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2." J Bacteriol 176(14);4416-23. PMID: 8021226

Sargent98: Sargent F, Ballantine SP, Rugman PA, Palmer T, Boxer DH (1998). "Reassignment of the gene encoding the Escherichia coli hydrogenase 2 small subunit--identification of a soluble precursor of the small subunit in a hypB mutant." Eur J Biochem 1998;255(3);746-54. PMID: 9738917

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

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

Other References Related to Gene Regulation

Chung13: Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S (2013). "dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLoS Comput Biol 9(10);e1003246. PMID: 24146601

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Richard99: Richard DJ, Sawers G, Sargent F, McWalter L, Boxer DH (1999). "Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli." Microbiology 145 ( Pt 10);2903-12. PMID: 10537212

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
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