Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: DNA adenine methyltransferase



Gene: yhdJ Accession Numbers: EG11498 (EcoCyc), b3262, ECK3249

Synonyms: ccrM

Regulation Summary Diagram: ?

Summary:
Overexpression of YdhJ leads to methylation of genomic DNA at the NsiI recognition sequence (5'-ATGCAT-3'), and partially purified YdhJ is shown to methylate this sequence to produce N6-methyladenine in the 3' adenine position of ATGCAT in vitro [Broadbent07].

ydhJ is not an essential gene, and overexpression of ydhJ does not alter cell morphology [Baba06, Broadbent07].

A retracted [Kossykh04] publication [Kossykh04a] claimed that the "CcrM" protein is a cell cycle-regulated DNA adenine methyltransferase that is essential for viability.

Locations: cytosol

Map Position: [3,409,675 -> 3,410,559] (73.49 centisomes)
Length: 885 bp / 294 aa

Molecular Weight of Polypeptide: 33.397 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010706 , DIP:DIP-12296N , EchoBASE:EB1461 , EcoGene:EG11498 , EcoliWiki:b3262 , ModBase:P28638 , OU-Microarray:b3262 , PortEco:yhdJ , Pride:P28638 , Protein Model Portal:P28638 , RefSeq:NP_417728 , RegulonDB:EG11498 , SMR:P28638 , String:511145.b3262 , UniProt:P28638

Relationship Links: InterPro:IN-FAMILY:IPR001091 , InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR002941 , Pfam:IN-FAMILY:PF01555 , Prints:IN-FAMILY:PR00508 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0032775 - DNA methylation on adenine Inferred by computational analysis Inferred from experiment [Broadbent07, GOA01a]
GO:0006306 - DNA methylation Inferred by computational analysis [GOA01]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity Inferred from experiment Inferred by computational analysis [GOA01a, Broadbent07]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008170 - N-methyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes

Essentiality data for yhdJ 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 ? 16-Apr-2007 by Keseler I , SRI International


Enzymatic reaction of: DNA adenine methyltransferase

EC Number: 2.1.1.72

a DNA adenine + S-adenosyl-L-methionine <=> S-adenosyl-L-homocysteine + a DNA 6-methylaminopurine + H+

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

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
S-adenosyl-L-methionine
12.0
[Bonnist12, BRENDA14]
S-adenosyl-L-methionine
5.6, 12.2
1.2e-4, 2.1e-4, 2.5e-4, 2.8e-4, 0.0012
[Bheemanaik06, BRENDA14]
a DNA adenine
0.023, 0.081
[Coffin08, BRENDA14]
a DNA adenine
0.3
[Bonnist12, BRENDA14]
a DNA adenine
0.003
[Coffin09, BRENDA14]
a DNA adenine
0.023, 0.081
0.0038, 0.015
[Coffin09a, BRENDA14]
a DNA adenine
0.0036, 0.017, 0.026, 0.12, 0.27, 0.8, 0.83, 0.91, 1.0, 7.1
9.6e-5, 0.0041, 0.0053, 0.0056, 0.021, 0.094, 0.1, 0.11, 0.12, 0.14, 0.14, 0.16, 0.17, 0.2, 0.23, 0.25, 0.27, 0.3, 0.32, 0.37, 0.45, 0.58, 0.93
[Bheemanaik06, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 28
[Ball92, UniProt10]
Alternate sequence: K → N; UniProt: (in Ref. 3; AAA23784);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3262 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11498; 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

Ball92: Ball CA, Osuna R, Ferguson KC, Johnson RC (1992). "Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli." J Bacteriol 1992;174(24);8043-56. PMID: 1459953

Bheemanaik06: Bheemanaik S, Reddy YV, Rao DN (2006). "Structure, function and mechanism of exocyclic DNA methyltransferases." Biochem J 399(2);177-90. PMID: 16987108

Bonnist12: Bonnist EY, Liebert K, Dryden DT, Jeltsch A, Jones AC (2012). "Using the fluorescence decay of 2-aminopurine to investigate conformational change in the recognition sequence of the EcoRV DNA-(adenine-N6)-methyltransferase on enzyme binding." Biophys Chem 160(1);28-34. PMID: 21962489

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Broadbent07: Broadbent SE, Balbontin R, Casadesus J, Marinus MG, van der Woude M (2007). "YhdJ, a non-essential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica." J Bacteriol 189(11):4325-7. PMID: 17400740

Coffin08: Coffin SR, Reich NO (2008). "Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences." J Biol Chem 283(29);20106-16. PMID: 18502761

Coffin09: Coffin SR, Reich NO (2009). "Escherichia coli DNA adenine methyltransferase: intrasite processivity and substrate-induced dimerization and activation." Biochemistry 48(31);7399-410. PMID: 19580332

Coffin09a: Coffin SR, Reich NO (2009). "Escherichia coli DNA adenine methyltransferase: the structural basis of processive catalysis and indirect read-out." J Biol Chem 284(27);18390-400. PMID: 19419959

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, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Kossykh04: Kossykh VG, Lloyd RS (2004). "A DNA adenine methyltransferase of Escherichia coli that is cell cycle regulated and essential for viability." J Bacteriol 186(18);6340. PMID: 15342609

Kossykh04a: Kossykh VG, Lloyd RS (2004). "A DNA adenine methyltransferase of Escherichia coli that is cell cycle regulated and essential for viability." J Bacteriol 186(7);2061-7. PMID: 15028690

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: 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 18.5 on Fri Dec 19, 2014, BIOCYC14B.