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Escherichia coli K-12 substr. MG1655 Protein: predicted hydrolase



Gene: ycaC Accession Numbers: EG11241 (EcoCyc), b0897, ECK0888

Regulation Summary Diagram: ?

Subunit composition of predicted hydrolase = [YcaC]8
         predicted hydrolase monomer = YcaC

Summary:
The crystal structure of YcaC, solved at 1.8 Å resolution, indicates that YcaC has similarity to hydrolases and forms a homooctamer (a dimer of tetrameric ring structures) [Colovos98]. The protein shows structural similarity to the pyrazinamidase encoded by the Pyrococcus horikoshii 999 gene [Du01].

Cys118 is identified as a likely catalytic residue [Colovos98].

Locations: cytosol, membrane

Map Position: [944,154 <- 944,780] (20.35 centisomes)
Length: 627 bp / 208 aa

Molecular Weight of Polypeptide: 23.1 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003050 , DIP:DIP-11462N , EchoBASE:EB1223 , EcoGene:EG11241 , EcoliWiki:b0897 , ModBase:P21367 , OU-Microarray:b0897 , PortEco:ycaC , Pride:P21367 , Protein Model Portal:P21367 , RefSeq:NP_415417 , RegulonDB:EG11241 , SMR:P21367 , String:511145.b0897 , UniProt:P21367

Relationship Links: InterPro:IN-FAMILY:IPR000868 , PDB:Structure:1YAC , Pfam:IN-FAMILY:PF00857

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for ycaC 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]

Credits:
Last-Curated ? 20-Nov-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Active-Site 118
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b0897 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11241; 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

Colovos98: Colovos C, Cascio D, Yeates TO (1998). "The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity." Structure 1998;6(10);1329-37. PMID: 9782055

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

Du01: Du X, Wang W, Kim R, Yakota H, Nguyen H, Kim SH (2001). "Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii." Biochemistry 2001;40(47);14166-72. PMID: 11714269

GOA01: 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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Nishino05: Nishino K, Honda T, Yamaguchi A (2005). "Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system." J Bacteriol 187(5);1763-72. PMID: 15716448


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 SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, BIOCYC14B.