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Escherichia coli K-12 substr. MG1655 Polypeptide: protein involved in processing of HyaA and HyaB proteins



Gene: hyaD Accession Numbers: EG10471 (EcoCyc), b0975, ECK0966

Regulation Summary Diagram: ?

Regulation summary diagram for hyaD

Summary:
The HyaD protein is required for the synthesis of active hydrogenase isoenzyme 1 (HYD1) [Menon91]. HyaD is similar to HybD, the maturation protease for hydrogenase 2 [Fritsche99]. It is therefore likely that HyaA is an endopeptidase required for maturation of hydrogenase 1.

Gene Citations: [Menon90, Maciag11]

Locations: cytosol

Map Position: [1,034,993 -> 1,035,580] (22.31 centisomes, 80°)
Length: 588 bp / 195 aa

Molecular Weight of Polypeptide: 21.546 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003292 , CGSC:31791 , DIP:DIP-9960N , EchoBASE:EB0466 , EcoGene:EG10471 , EcoliWiki:b0975 , Mint:MINT-1321337 , ModBase:P19930 , OU-Microarray:b0975 , PortEco:hyaD , PR:PRO_000022945 , Protein Model Portal:P19930 , RefSeq:NP_415494 , RegulonDB:EG10471 , SMR:P19930 , String:511145.b0975 , UniProt:P19930

Relationship Links: InterPro:IN-FAMILY:IPR000671 , InterPro:IN-FAMILY:IPR004419 , InterPro:IN-FAMILY:IPR023430 , Pfam:IN-FAMILY:PF01750 , Prints:IN-FAMILY:PR00446

In Paralogous Gene Group: 447 (3 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for hyaD

GO Terms:

Biological Process: GO:0016485 - protein processing Inferred from experiment Inferred by computational analysis [GOA01a, Menon91]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a]
GO:0043085 - positive regulation of catalytic activity Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0004190 - aspartic-type endopeptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008047 - enzyme activator activity Inferred by computational analysis [GOA01a]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase 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 aerobic respiration
metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for hyaD knockouts: ?

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

Sequence Features

Protein sequence of protein involved in processing of HyaA and HyaB proteins with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 19
[UniProt10a]
UniProt: Nickel; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 65
[UniProt10a]
UniProt: Nickel; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 96
[UniProt10a]
UniProt: Nickel; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b0975 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10471; confirmed by SwissProt match.


References

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

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

Fritsche99: Fritsche E, Paschos A, Beisel HG, Bock A, Huber R (1999). "Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli." J Mol Biol 288(5);989-98. PMID: 10331925

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

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Menon90: Menon NK, Robbins J, Peck HD, Chatelus CY, Choi ES, Przybyla AE (1990). "Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames." J Bacteriol 1990;172(4);1969-77. PMID: 2180913

Menon91: Menon NK, Robbins J, Wendt JC, Shanmugam KT, Przybyla AE (1991). "Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1." J Bacteriol 173(15);4851-61. PMID: 1856178

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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

Atlung97: Atlung T, Knudsen K, Heerfordt L, Brondsted L (1997). "Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation." J Bacteriol 179(7);2141-6. PMID: 9079897

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Brondsted94: Brondsted L, Atlung T (1994). "Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli." J Bacteriol 176(17);5423-8. PMID: 8071220

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

King99: King PW, Przybyla AE (1999). "Response of hya expression to external pH in Escherichia coli." J Bacteriol 181(17);5250-6. PMID: 10464194

Nesbit12: Nesbit AD, Fleischhacker AS, Teter SJ, Kiley PJ (2012). "ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli." J Bacteriol 194(24);6892-9. PMID: 23065979

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

Yamanaka14: Yamanaka Y, Oshima T, Ishihama A, Yamamoto K (2014). "Characterization of the YdeO regulon in Escherichia coli." PLoS One 9(11);e111962. PMID: 25375160


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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 Mon Aug 3, 2015, biocyc12.