Escherichia coli K-12 substr. MG1655 Enzyme: hydrogenase maturation protein, carbamoyltransferase

Gene: hypF Accession Numbers: EG11551 (EcoCyc), b2712, ECK2707

Synonyms: hydA

Regulation Summary Diagram: ?

Regulation summary diagram for hypF

HypF is one of a number of proteins required for maturation of hydrogenase 1, hydrogenase 2 and hydrogenase 3 [Maier96, Maier96a, Soboh10].

In the absence of other substrates, HypF hydrolyzes carbamoyl phosphate [Paschos02]. However, under physiological conditions in the presence of HypE, HypF functions as a carbamoyl transferase, generating HypE-S-carboxamide at the C-terminal cysteine residue of HypE [Reissmann03]. This reaction may involve the formation of a carbamoyladenylate intermediate [Petkun11]. During the carbamoyl transfer reaction, HypE and HypF form a tight stochiometric complex [Blokesch04]; the interaction has been characterized in detail [Rangarajan08].

Crystal structures of HypF lacking the N-terminal acylphosphatase domain have been solved. Mutations in the N-terminal nucleotide-binding site 1 abolished the hydrogenase maturation activity of HypF; the C-terminal nucleotide-binding site 2 is also required for full activity [Petkun11].

The N-terminal acylphosphatase domain of HypF forms amyloid-like protein aggregates under certain conditions [Chiti01], and its folding and toxicity have been studied; e.g. see [Calloni03, Campioni08, Campioni10]. Crystal structures of this domain have been solved at 1.3 Å resolution [Rosano02].

A hypF in-frame deletion mutant lacks significant hydrogenase activity due to defects in hydrogenase maturation [Maier96]. A hypF insertion mutant lacking all hydrogenase activity shows significantly decreased acid resistance during stationary phase [Hayes06].

The hydN-hypF operon is maximally transcribed under anaerobic conditions in the presence of formate and is dependent on FhlA [Maier96].

HypF: "affect the activity of all three hydrogenases in a pleiotropic manner"

Review: [Forzi07]

Gene Citations: [Shimada05]

Locations: cytosol

Map Position: [2,833,195 <- 2,835,447] (61.06 centisomes, 220°)
Length: 2253 bp / 750 aa

Molecular Weight of Polypeptide: 82.066 kD (from nucleotide sequence), 80.0 kD (experimental) [Paschos02 ]

Unification Links: ASAP:ABE-0008915 , CGSC:18232 , DIP:DIP-10000N , EchoBASE:EB1512 , EcoGene:EG11551 , EcoliWiki:b2712 , Mint:MINT-1276849 , ModBase:P30131 , OU-Microarray:b2712 , PortEco:hypF , PR:PRO_000022977 , Pride:P30131 , Protein Model Portal:P30131 , RefSeq:NP_417192 , RegulonDB:EG11551 , SMR:P30131 , String:511145.b2712 , UniProt:P30131

Relationship Links: InterPro:IN-FAMILY:IPR001792 , InterPro:IN-FAMILY:IPR004421 , InterPro:IN-FAMILY:IPR006070 , InterPro:IN-FAMILY:IPR011125 , InterPro:IN-FAMILY:IPR017945 , InterPro:IN-FAMILY:IPR017968 , Panther:IN-FAMILY:PTHR10029:SF4 , PDB:Structure:1GXT , PDB:Structure:1GXU , Pfam:IN-FAMILY:PF00708 , Pfam:IN-FAMILY:PF01300 , Pfam:IN-FAMILY:PF07503 , Prosite:IN-FAMILY:PS00150 , Prosite:IN-FAMILY:PS51160 , Prosite:IN-FAMILY:PS51163

In Paralogous Gene Group: 268 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for hypF

GO Terms:

Biological Process: GO:0046944 - protein carbamoylation Inferred from experiment Inferred by computational analysis [GOA01a, Reissmann03]
GO:0051604 - protein maturation Inferred from experiment [Maier96a, Maier96]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment Inferred by computational analysis [GOA01a, Petkun11]
GO:0016743 - carboxyl- or carbamoyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, Reissmann03]
GO:0003725 - double-stranded RNA binding Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
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 hypF 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 ? 20-Dec-2011 by Keseler I , SRI International

Enzymatic reaction of: carbamoyltransferase

EC Number: 6.1.2.-

carbamoyl-phosphate + HypE + ATP + H2O <=> a HypE hydrogenase maturation protein-S-carboxamide + AMP + diphosphate + phosphate

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 maturation protein, carbamoyltransferase with features indicated

Feature Class Location Citations Comment
Conserved-Region 8 -> 92
UniProt: Acylphosphatase-like;
Protein-Segment 19 -> 23
UniProt: Binds to substrate; phosphate group; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 23
[Blokesch04, UniProt11]
[Blokesch04, UniProt11]
R → Q: Diminishes activity.
R → E, H or K: Loss of activity.
Sequence-Conflict 31 -> 32
[Tomiyama93, UniProt15]
UniProt: (in Ref. 1; BAA03315).
Zn-Finger-Region 109 -> 134
UniProt: C4-type; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 112
[Paschos02, UniProt15]
UniProt: Loss of activity.
Zn-Finger-Region 159 -> 184
UniProt: C4-type; Non-Experimental Qualifier: potential;
Mutagenesis-Variant 162
[Paschos02, UniProt15]
UniProt: Loss of activity.
Conserved-Region 200 -> 376
UniProt: YrdC-like;
Sequence-Conflict 367 -> 386
[Tomiyama93, UniProt15]
UniProt: (in Ref. 1; BAA03315).
Sequence-Conflict 431 -> 432
[Tomiyama93, UniProt15]
UniProt: (in Ref. 1; BAA03315).
Sequence-Conflict 435
[Tomiyama93, UniProt15]
UniProt: (in Ref. 1; BAA03315).
Mutagenesis-Variant 475
[Paschos02, UniProt15]
UniProt: Loss of activity.
Mutagenesis-Variant 476
[Blokesch04, UniProt11]
UniProt: Carbamoyl phosphate-dependent ATP hydrolysis activity diminished in vitro but sufficient for wild-type-like phenotype.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2712 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11551; 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

Blokesch04: Blokesch M, Paschos A, Bauer A, Reissmann S, Drapal N, Bock A (2004). "Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE." Eur J Biochem 271(16);3428-36. PMID: 15291820

Calloni03: Calloni G, Taddei N, Plaxco KW, Ramponi G, Stefani M, Chiti F (2003). "Comparison of the folding processes of distantly related proteins. Importance of hydrophobic content in folding." J Mol Biol 330(3);577-91. PMID: 12842473

Campioni08: Campioni S, Mossuto MF, Torrassa S, Calloni G, de Laureto PP, Relini A, Fontana A, Chiti F (2008). "Conformational properties of the aggregation precursor state of HypF-N." J Mol Biol 379(3);554-67. PMID: 18466920

Campioni10: Campioni S, Mannini B, Zampagni M, Pensalfini A, Parrini C, Evangelisti E, Relini A, Stefani M, Dobson CM, Cecchi C, Chiti F (2010). "A causative link between the structure of aberrant protein oligomers and their toxicity." Nat Chem Biol 6(2);140-7. PMID: 20081829

Chiti01: Chiti F, Bucciantini M, Capanni C, Taddei N, Dobson CM, Stefani M (2001). "Solution conditions can promote formation of either amyloid protofilaments or mature fibrils from the HypF N-terminal domain." Protein Sci 10(12);2541-7. PMID: 11714922

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."

Hayes06: Hayes ET, Wilks JC, Sanfilippo P, Yohannes E, Tate DP, Jones BD, Radmacher MD, BonDurant SS, Slonczewski JL (2006). "Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12." BMC Microbiol 6;89. PMID: 17026754

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

Maier96: Maier T, Binder U, Bock A (1996). "Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism." Arch Microbiol 1996;165(5);333-41. PMID: 8661925

Maier96a: Maier T, Bock A (1996). "Generation of active [NiFe] hydrogenase in vitro from a nickel-free precursor form." Biochemistry 35(31);10089-93. PMID: 8756471

Paschos02: Paschos A, Bauer A, Zimmermann A, Zehelein E, Bock A (2002). "HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation." J Biol Chem 277(51);49945-51. PMID: 12377778

Petkun11: Petkun S, Shi R, Li Y, Asinas A, Munger C, Zhang L, Waclawek M, Soboh B, Sawers RG, Cygler M (2011). "Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites." Structure 19(12);1773-83. PMID: 22153500

Rangarajan08: Rangarajan ES, Asinas A, Proteau A, Munger C, Baardsnes J, Iannuzzi P, Matte A, Cygler M (2008). "Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF." J Bacteriol 190(4);1447-58. PMID: 18065529

Reissmann03: Reissmann S, Hochleitner E, Wang H, Paschos A, Lottspeich F, Glass RS, Bock A (2003). "Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands." Science 299(5609);1067-70. PMID: 12586941

Rosano02: Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M (2002). "Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain." J Mol Biol 321(5);785-96. PMID: 12206761

Shimada05: Shimada T, Fujita N, Maeda M, Ishihama A (2005). "Systematic search for the Cra-binding promoters using genomic SELEX system." Genes Cells 10(9);907-18. PMID: 16115199

Soboh10: Soboh B, Kruger S, Kuhns M, Pinske C, Lehmann A, Sawers RG (2010). "Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 of Escherichia coli." FEBS Lett 584(18);4109-14. PMID: 20807532

Tomiyama93: Tomiyama M., Shiotani M., Nishio M., Ikebukuro K., Sode K., Tamiya E., Karube I. (1993). "Nucleotide sequence and functional analysis of hydA of E.coli." Data submission to EMBL/GenBank/DDBJ databases on 1993-02.

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

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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

Pruss01: Pruss BM, Liu X, Hendrickson W, Matsumura P (2001). "FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions." FEMS Microbiol Lett 2001;197(1);91-7. PMID: 11287152

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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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