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Escherichia coli K-12 substr. MG1655 Enzyme: protein-(glutamine-N5) methyltransferase



Gene: prmC Accession Numbers: EG12424 (EcoCyc), b1212, ECK1200

Synonyms: hemK

Regulation Summary Diagram: ?

Summary:
PrmC is a protein-(glutamine-N5) methyltransferase that shows activity toward polypeptide chain release factors RF1 and RF2 [Nakahigashi02, HeurgueHamard02]. PrmC was initially reported to be a putative protoporphyrinogen oxidase, based on genetic experiments [Nakayashiki95].

The crystal structure of PrmC is reported at 3.2 Å resolution [Yang04a]. The N terminus may determine methyltransferase substrate specificity [Bujnicki99], and the structure of the putative substrate binding domains of the E. coli and Thermotoga maritima proteins are similar despite their lack of sequence similarity [Yang04a]. The C terminus of the Thermotoga maritima protein contains the active site, and the structure illustrates similarities to DNA methyltransferases within this catalytic region [Schubert03]. The catalytic mechanism is discussed [Schubert03].

A mutant shows a defect in nonsense codon recognition [Nakahigashi02], defects in ribosome progression [Nakahigashi02], and a growth defect [Nakayashiki95] that is suppressed by mutations in polypeptide chain release factor RF2 [Nakahigashi02, HeurgueHamard02]. A mutant shows a defect in heme synthesis from 5-aminolevulinic acid [Nakayashiki95]. A mutant exhibits a global transcription pattern characteristic of anaerobic growth, which may decrease oxidative stress and therefore account for the genetic results originally thought to be indicative of a PrmC role in heme synthesis [Nakahigashi02].

The PrmC/HemK family of proteins shows similarity to gamma subfamily S-adenosyl-methionine-dependent adenine-specific DNA methyltransferases [Bujnicki99]. PrmB and PrmC have sequence similarity to each other; PrmB is active toward ribosomal protein L3, whereas PrmC is active toward polypeptide chain release factors RF1 and RF2 [HeurgueHamard02].

Citations: [Clarke02]

Gene Citations: [Verkamp89, Dahlgren04]

Locations: cytosol

Map Position: [1,265,317 -> 1,266,150] (27.27 centisomes)
Length: 834 bp / 277 aa

Molecular Weight of Polypeptide: 30.975 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004068 , CGSC:36992 , EchoBASE:EB2323 , EcoGene:EG12424 , EcoliWiki:b1212 , ModBase:P0ACC1 , OU-Microarray:b1212 , PortEco:prmC , PR:PRO_000022877 , Protein Model Portal:P0ACC1 , RefSeq:NP_415730 , RegulonDB:EG12424 , SMR:P0ACC1 , String:511145.b1212 , UniProt:P0ACC1

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR004556 , InterPro:IN-FAMILY:IPR019874 , InterPro:IN-FAMILY:IPR025714 , PDB:Structure:1T43 , PDB:Structure:2B3T , Pfam:IN-FAMILY:PF13847

In Paralogous Gene Group: 261 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006415 - translational termination Inferred from experiment [Khalid11]
GO:0006479 - protein methylation Inferred from experiment Inferred by computational analysis [GOA01, Khalid11]
GO:0010468 - regulation of gene expression Inferred from experiment [Khalid11]
GO:0018364 - peptidyl-glutamine methylation Inferred from experiment Inferred by computational analysis [GOA06, HeurgueHamard02]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0008276 - protein methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, Khalid11]
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity Inferred from experiment [Khalid11]
GO:0036009 - protein-glutamine N-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, HeurgueHamard02]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer protein related posttranslational modification

Essentiality data for prmC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Enzymatic reaction of: protein-(glutamine-N5) methyltransferase

EC Number: 2.1.1.297

a [release factor]-L-glutamine + S-adenosyl-L-methionine <=> a [release factor]-N5-methyl-L-glutamine + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Summary:
PrmC is a protein-(glutamine-N5) methyltransferase that shows activity toward polypeptide chain release factors RF1 and RF2, which are methylated on the GGQ motif [Nakahigashi02, HeurgueHamard02].

PrmB and PrmC have sequence similarity to each other; PrmB is active toward ribosomal protein L3, whereas PrmC is active toward polypeptide chain release factors RF1 and RF2 [HeurgueHamard02].


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 36
[Graille05, UniProt12a]
Alternate sequence: R → A; UniProt: 17% of wild-type RF1 methylation activity.
Mutagenesis-Variant 40
[Graille05, UniProt12a]
Alternate sequence: L → A; UniProt: 60% of wild-type RF1 methylation activity.
Mutagenesis-Variant 41
[Graille05, UniProt11]
Alternate sequence: A → R; UniProt: Strongly reduced affinity for S- adenosyl-L-methionine.
Mutagenesis-Variant 42
[Graille05, UniProt12a]
Alternate sequence: F → A; UniProt: 40% of wild-type RF1 methylation activity.
Mutagenesis-Variant 44
[Graille05, UniProt12a]
Alternate sequence: E → R; UniProt: 33% of wild-type RF1 methylation activity.
Alternate sequence: E → A; UniProt: 62% of wild-type RF1 methylation activity.
Protein-Segment 117 -> 121
[UniProt10a]
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 140
[UniProt10]
UniProt: S-adenosyl-L-methionine;
Amino-Acid-Sites-That-Bind 168
[UniProt10]
UniProt: S-adenosyl-L-methionine;
Mutagenesis-Variant 183
[Graille05, UniProt11]
Alternate sequence: N → A; UniProt: Reduces activity by over 98%.
Amino-Acid-Sites-That-Bind 183
[UniProt10]
UniProt: S-adenosyl-L-methionine;
Protein-Segment 183 -> 186
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b1212 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12424; 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

Bujnicki99: Bujnicki JM, Radlinska M (1999). "Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases? A hypothesis." IUBMB Life 48(3);247-9. PMID: 10690633

Clarke02: Clarke S (2002). "The methylator meets the terminator." Proc Natl Acad Sci U S A 99(3);1104-6. PMID: 11830650

Dahlgren04: Dahlgren A, Ryden-Aulin M (2004). "Effects of two cis-acting mutations on the regulation and expression of release factor one in Escherichia coli." Biochimie 86(7);431-8. PMID: 15308332

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

GOA01: 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."

Graille05: Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH (2005). "Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC." Mol Cell 20(6);917-27. PMID: 16364916

HeurgueHamard02: Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH (2002). "The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors." EMBO J 21(4);769-78. PMID: 11847124

Khalid11: Khalid U, Khalil S (2011). "Ethical dilemma of recovering organs before donor death." Exp Clin Transplant 9(4);284-5. PMID: 21819377

Nakahigashi02: Nakahigashi K, Kubo N, Narita S, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H (2002). "HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination." Proc Natl Acad Sci U S A 99(3);1473-8. PMID: 11805295

Nakayashiki95: Nakayashiki T, Nishimura K, Inokuchi H (1995). "Cloning and sequencing of a previously unidentified gene that is involved in the biosynthesis of heme in Escherichia coli." Gene 153(1);67-70. PMID: 7883187

Schubert03: Schubert HL, Phillips JD, Hill CP (2003). "Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase." Biochemistry 42(19);5592-9. PMID: 12741815

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

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

Verkamp89: Verkamp E, Chelm BK (1989). "Isolation, nucleotide sequence, and preliminary characterization of the Escherichia coli K-12 hemA gene." J Bacteriol 171(9);4728-35. PMID: 2548996

Yang04a: Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X (2004). "Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase." J Mol Biol 340(4);695-706. PMID: 15223314

Other References Related to Gene Regulation

Choi96: Choi P, Wang L, Archer CD, Elliott T (1996). "Transcription of the glutamyl-tRNA reductase (hemA) gene in Salmonella typhimurium and Escherichia coli: role of the hemA P1 promoter and the arcA gene product." J Bacteriol 1996;178(3);638-46. PMID: 8550494

Darie94: Darie S, Gunsalus RP (1994). "Effect of heme and oxygen availability on hemA gene expression in Escherichia coli: role of the fnr, arcA, and himA gene products." J Bacteriol 1994;176(17);5270-6. PMID: 8071201

Melville96: Melville SB, Gunsalus RP (1996). "Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes." Proc Natl Acad Sci U S A 93(3);1226-31. PMID: 8577745


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 Nov 21, 2014, BIOCYC14A.