Escherichia coli K-12 substr. MG1655 Polypeptide: host modification; DNA methylase M

Gene: hsdM Accession Numbers: EG10458 (EcoCyc), b4349, ECK4339

Synonyms: hsm, hsp

Regulation Summary Diagram: ?

Regulation summary diagram for hsdM

Component of: EcoKI restriction-modification system (extended summary available)

HsdM is the modification methyltransferase component of the EcoKI restriction-modification system [Sain80].

Locations: cytosol

Map Position: [4,579,482 <- 4,581,071] (98.7 centisomes, 355°)
Length: 1590 bp / 529 aa

Molecular Weight of Polypeptide: 59.307 kD (from nucleotide sequence), 62 kD (experimental) [Sain80 ]

Unification Links: ASAP:ABE-0014260 , CGSC:621 , DIP:DIP-9943N , EchoBASE:EB0453 , EcoGene:EG10458 , EcoliWiki:b4349 , Mint:MINT-1252160 , ModBase:P08957 , OU-Microarray:b4349 , PortEco:hsdM , PR:PRO_000022928 , Pride:P08957 , Protein Model Portal:P08957 , RefSeq:NP_418769 , RegulonDB:EG10458 , SMR:P08957 , String:511145.b4349 , UniProt:P08957

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR002296 , InterPro:IN-FAMILY:IPR003356 , InterPro:IN-FAMILY:IPR022749 , InterPro:IN-FAMILY:IPR029063 , PDB:Structure:2AR0 , PDB:Structure:2Y7C , PDB:Structure:2Y7H , Pfam:IN-FAMILY:PF02384 , Pfam:IN-FAMILY:PF12161 , Prints:IN-FAMILY:PR00507 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006306 - DNA methylation Inferred by computational analysis [GOA01a]
GO:0009307 - DNA restriction-modification system Inferred by computational analysis [UniProtGOA11a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0032775 - DNA methylation on adenine Inferred by computational analysis [GOA01]
Molecular Function: GO:0008170 - N-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, Willcock94]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer DNA related DNA restriction/modification
regulation type of regulation DNA structure level methylation

Essentiality data for hsdM 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]

Subunit of: EcoKI restriction-modification system

Subunit composition of EcoKI restriction-modification system = [HsdM]2[HsdR]2[HsdS]
         host modification; DNA methylase M = HsdM (summary available)
         host restriction; endonuclease R = HsdR (summary available)
         specificity determinant for hsdM and hsdR = HsdS (summary available)

EcoKI is the type IA restriction-modification enzyme complex responsible for identifying and restricting unmethylated, foreign DNA and for modifying native, hemimethylated DNA by methylation for self-identification. The three proteins which make up EcoKI-HsdR, HsdM, and HsdS-are all required for restriction. There is a complex that can form-HsdM2HsdS1-with only methyltransferase activity. HsdM and HsdS are required for methylation. HsdM contains a methyltransferase active site and a site for cofactor binding. The cofactor S-adenosylmethionine (AdoMet) acts as the methyl donor for modification. Hemimethylated DNA is preferred over unmethylated DNA as substrate for modification. Interaction of HsdS with DNA requires HsdM. HsdS contains two target recognition domains which recognize the sequence 5'AAC(N6)GTGC. One recognizes the AAC sequence, while the other recognizes the GTGC sequence. HsdR couples DNA translocation to ATP hydrolysis and contains the catalytic site for restriction of the DNA. When the EcoKI binds its target sequence, it makes another contact with the DNA which begins translocation of the DNA while still remaining bound to the target sequence, creating loops. Restriction occurs when translocation becomes stalled because enzymes run into each other, when DNA becomes too supercoiled, when the loop of DNA between two dimerized enzymes becomes taut, and when the enzyme becomes blocked, such as at Holliday junctions. Endonucleolytic activity requires Mg2+, ATP, and AdoMet [Murray00, Loenen03].

Created 05-Apr-2006 by Johnson A , TIGR

Enzymatic reaction of: type I site-specific deoxyribonuclease (EcoKI restriction-modification system)

EC Number:

ATP + DNAn + H2O <=> a double stranded DNA with 5'-terminal phosphate + ADP + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of host modification; DNA methylase M with features indicated

Feature Class Location Citations Comment
Protein-Segment 148 -> 153
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Protein-Segment 178 -> 180
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 216
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4349 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10458; confirmed by SwissProt match.


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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Loenen03: Loenen WA (2003). "Tracking EcoKI and DNA fifty years on: a golden story full of surprises." Nucleic Acids Res 31(24);7059-69. PMID: 14654681

Murray00: Murray NE (2000). "Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)." Microbiol Mol Biol Rev 64(2);412-34. PMID: 10839821

Sain80: Sain B, Murray NE (1980). "The hsd (host specificity) genes of E. coli K 12." Mol Gen Genet 180(1);35-46. PMID: 6255295

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."

Willcock94: Willcock DF, Dryden DT, Murray NE (1994). "A mutational analysis of the two motifs common to adenine methyltransferases." EMBO J 13(16);3902-8. PMID: 8070417

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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 Tue Oct 6, 2015, biocyc14.