Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: methionine-oxo-acid transaminase, PLP-dependent



Gene: ybdL Accession Numbers: G6329 (EcoCyc), b0600, ECK0594

Regulation Summary Diagram: ?

Summary:
YbdL is an aminotransferase with a preference for methionine followed by histidine and phenylalanine. A crystal structure of YbdL was solved at 2.35 Å resolution, showing a typical aspartate aminotransferase fold. YbdL contains a covalently bound pyridoxal-5'-phosphate at the conserved active site residue Lys236 [Dolzan04].

Expression of ybdL is increased by exposure to S-nitrosoglutathione in defined medium under aerobic conditions [Flatley05].

Locations: cytosol

Map Position: [632,809 -> 633,969] (13.64 centisomes)
Length: 1161 bp / 386 aa

Molecular Weight of Polypeptide: 42.963 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002069 , DIP:DIP-11350N , EchoBASE:EB3302 , EcoGene:EG13531 , EcoliWiki:b0600 , Mint:MINT-1306557 , ModBase:P77806 , OU-Microarray:b0600 , PortEco:ybdL , Pride:P77806 , Protein Model Portal:P77806 , RefSeq:NP_415133 , RegulonDB:G6329 , SMR:P77806 , String:511145.b0600 , UniProt:P77806

Relationship Links: InterPro:IN-FAMILY:IPR004839 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , PDB:Structure:1U08 , Pfam:IN-FAMILY:PF00155 , Prosite:IN-FAMILY:PS00105

In Paralogous Gene Group: 163 (5 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0010326 - methionine-oxo-acid transaminase activity Inferred from experiment [Dolzan04]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA01, Dolzan04]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008483 - transaminase activity Inferred by computational analysis [UniProtGOA11]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

Gene Class: UNCLASSIFIED

Essentiality data for ybdL 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]

Credits:
Last-Curated ? 06-Apr-2010 by Keseler I , SRI International


Enzymatic reaction of: methionine-oxo-acid transaminase

Synonyms: methionine aminotransferase

EC Number: 2.6.1.88

L-methionine + a 2-oxo carboxylate <=> 2-oxo-4-methylthiobutanoate + a standard α amino acid

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Alternative Substrates for L-methionine: L-histidine [Dolzan04 ] , L-phenylalanine [Dolzan04 ]

Summary:
Only the first half reaction, transfer of the amino group from the amino acid to the PLP cofactor of the enzyme, has been experimentally measured [Dolzan04].

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Dolzan04]


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 236
[UniProt11]
UniProt: N6-(pyridoxal phosphate)lysine.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Dolzan04: Dolzan M, Johansson K, Roig-Zamboni V, Campanacci V, Tegoni M, Schneider G, Cambillau C (2004). "Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function." FEBS Lett 571(1-3);141-6. PMID: 15280032

Flatley05: Flatley J, Barrett J, Pullan ST, Hughes MN, Green J, Poole RK (2005). "Transcriptional responses of Escherichia coli to S-nitrosoglutathione under defined chemostat conditions reveal major changes in methionine biosynthesis." J Biol Chem 280(11);10065-72. PMID: 15647275

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, 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

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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 18.5 on Mon Nov 24, 2014, BIOCYC13B.