Escherichia coli K-12 substr. MG1655 Protein: carboxylate-amine ligase

Gene: ybdK Accession Numbers: G6326 (EcoCyc), b0581, ECK0573

Regulation Summary Diagram: ?

Regulation summary diagram for ybdK

Subunit composition of carboxylate-amine ligase = [YbdK]2
         carboxylate-amine ligase = YbdK

YbdK is a carboxylate-amine ligase; it can catalyze the ligation of glutamate with cysteine at a low catalytic rate. The enzyme binds ATP in a Mg2+-dependent manner [Lehmann04].

A crystal structure of YbdK was solved at 2.15 Å resolution, showing a fold similar to glutamine synthetase, but suggesting a different substrate specificity [Lehmann04].

Locations: cytosol

Map Position: [605,488 <- 606,606] (13.05 centisomes, 47°)
Length: 1119 bp / 372 aa

Molecular Weight of Polypeptide: 41.688 kD (from nucleotide sequence)

Molecular Weight of Multimer: 72.0 kD (experimental) [Lehmann04]

Unification Links: ASAP:ABE-0001992 , EchoBASE:EB3408 , EcoGene:EG13644 , EcoliWiki:b0581 , OU-Microarray:b0581 , PortEco:ybdK , Protein Model Portal:P77213 , RefSeq:NP_415113 , RegulonDB:G6326 , SMR:P77213 , String:511145.b0581 , UniProt:P77213

Relationship Links: InterPro:IN-FAMILY:IPR006336 , InterPro:IN-FAMILY:IPR011793 , PDB:Structure:1R8G , Pfam:IN-FAMILY:PF04107

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0042398 - cellular modified amino acid biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016879 - ligase activity, forming carbon-nitrogen bonds Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Lehmann04]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004357 - glutamate-cysteine ligase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for ybdK 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]

Created 16-Dec-2009 by Keseler I , SRI International
Last-Curated ? 21-Nov-2013 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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."

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

Lehmann04: Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O (2004). "YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays." Proteins 56(2);376-83. PMID: 15211520

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

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

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 19.0 on Wed Oct 7, 2015, biocyc12.