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: 16S rRNA m5C967 methyltransferase



Gene: rsmB Accession Numbers: EG12163 (EcoCyc), b3289, ECK3275

Synonyms: yhdB, rrmB, fmu, fmv, sun

Regulation Summary Diagram: ?

Summary:
RsmB is the methyltransferase responsible for methylation of 16S rRNA at the C967 nucleotide [Tscherne99, Gu99]. In vitro, the enzyme is active on free 16S rRNA, but not 30S ribosomal subunits [Negre89, Tscherne99, Gu99]. Methylation of G966 and C967 in 16S rRNA appears to stabilize the binding of initiator tRNA to the 30S pre-initiation complex prior to recognition of the start codon, thus modulating the early stages of translation initiation [Burakovsky12].

The crystal structure of the apoenzyme has been solved at 1.65 Å resolution, and that of the enzyme complexed with AdoMet at 2.1 Å resolution [Foster03].

A null mutation in rsmB has no significant effect on the growth rate in rich or minimal media [Gu99], although competitive growth experiments reveal a fitness defect [Burakovsky12]. Deletion of rsmB alters the initiation frequency from certain translation initiation codons [Arora13]. A C375A mutant is catalytically inactive, while a C325A mutant retains activity [Liu00b].

RsmB: "rRNA small subunit methyltransferase B"

Review: [Motorin10]

Locations: cytosol

Map Position: [3,433,229 -> 3,434,518] (74.0 centisomes)
Length: 1290 bp / 429 aa

Molecular Weight of Polypeptide: 48.348 kD (from nucleotide sequence), 47.0 kD (experimental) [Gu99 ]

Unification Links: ASAP:ABE-0010785 , DIP:DIP-10946N , EchoBASE:EB2082 , EcoGene:EG12163 , EcoliWiki:b3289 , ModBase:P36929 , OU-Microarray:b3289 , PortEco:rsmB , PR:PRO_000023882 , Pride:P36929 , Protein Model Portal:P36929 , RefSeq:NP_417747 , RegulonDB:EG12163 , SMR:P36929 , String:511145.b3289 , UniProt:P36929

Relationship Links: InterPro:IN-FAMILY:IPR001678 , InterPro:IN-FAMILY:IPR004573 , InterPro:IN-FAMILY:IPR006027 , InterPro:IN-FAMILY:IPR018314 , InterPro:IN-FAMILY:IPR023267 , InterPro:IN-FAMILY:IPR023541 , PDB:Structure:1J4F , PDB:Structure:1SQF , PDB:Structure:1SQG , Pfam:IN-FAMILY:PF01029 , Pfam:IN-FAMILY:PF01189 , Prints:IN-FAMILY:PR02008 , Prosite:IN-FAMILY:PS01153 , Prosite:IN-FAMILY:PS51686

In Paralogous Gene Group: 514 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0070475 - rRNA base methylation Inferred from experiment [Gu99]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01a]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0031167 - rRNA methylation Inferred by computational analysis [GOA06]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009383 - rRNA (cytosine-C5-)-methyltransferase activity Inferred from experiment [Tscherne99]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008649 - rRNA methyltransferase activity Inferred by computational analysis [GOA01a]
GO:0016434 - rRNA (cytosine) methyltransferase activity Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rsmB 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 ? 03-Apr-2013 by Keseler I , SRI International


Enzymatic reaction of: 16S rRNA m5C967 methyltransferase

Synonyms: rRNA SAM-dependent methyltransferase, ribosomal RNA small subunit methyltransferase B, rRNA small subunit methyltransferase B

EC Number: 2.1.1.176

cytosine967 in 16S rRNA + S-adenosyl-L-methionine <=> 5-methylcytosine967 in 16S rRNA + 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.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
cytosine967 in 16S rRNA
0.67
0.012
[Gu99, BRENDA14]


Sequence Features

Feature Class Location Common Name Citations Comment
Sequence-Conflict 3  
[Tscherne99, UniProt10a]
Alternate sequence: K → W; UniProt: (in Ref. 6; AA sequence);
Alternate sequence: K → C; UniProt: (in Ref. 6; AA sequence);
Sequence-Conflict 105 -> 106  
[Meinnel93, UniProt10a]
Alternate sequence: GA → RR; UniProt: (in Ref. 1; CAA54369);
Protein-Segment 254 -> 260  
[UniProt10]
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 277  
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Amino-Acid-Sites-That-Bind 303  
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Amino-Acid-Sites-That-Bind 322  
[UniProt10a]
UniProt: S-adenosyl-L-methionine;
Mutagenesis-Variant 325  
[Foster03, Liu00b, UniProt11]
Alternate sequence: C → A; UniProt: Reduces activity 3-fold.
Mutagenesis-Variant 375  
[Foster03, Liu00b, UniProt11]
Alternate sequence: C → A; UniProt: Loss of activity.
Active-Site 375 catalytic nucleophile
[Liu00b, Foster03]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
3/2/1998 (pkarp) Merged genes G810/b3289 and EG12163/sun
10/20/97 Gene b3289 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12163; confirmed by SwissProt match.


References

Arora13: Arora S, Bhamidimarri SP, Bhattacharyya M, Govindan A, Weber MH, Vishveshwara S, Varshney U (2013). "Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli." Nucleic Acids Res. PMID: 23530111

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

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

Burakovsky12: Burakovsky DE, Prokhorova IV, Sergiev PV, Milon P, Sergeeva OV, Bogdanov AA, Rodnina MV, Dontsova OA (2012). "Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation." Nucleic Acids Res 40(16);7885-95. PMID: 22649054

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

Foster03: Foster PG, Nunes CR, Greene P, Moustakas D, Stroud RM (2003). "The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate." Structure (Camb) 11(12);1609-20. PMID: 14656444

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

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."

Gu99: Gu XR, Gustafsson C, Ku J, Yu M, Santi DV (1999). "Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli." Biochemistry 38(13);4053-7. PMID: 10194318

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

Liu00b: Liu Y, Santi DV (2000). "m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts." Proc Natl Acad Sci U S A 97(15);8263-5. PMID: 10899996

Meinnel93: Meinnel T, Guillon JM, Mechulam Y, Blanquet S (1993). "The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control." J Bacteriol 175(4);993-1000. PMID: 8432722

Motorin10: Motorin Y, Lyko F, Helm M (2010). "5-methylcytosine in RNA: detection, enzymatic formation and biological functions." Nucleic Acids Res 38(5);1415-30. PMID: 20007150

Negre89: Negre D, Weitzmann C, Ofengand J (1989). "In vitro methylation of Escherichia coli 16S ribosomal RNA and 30S ribosomes." Proc Natl Acad Sci U S A 86(13);4902-6. PMID: 2662188

Tscherne99: Tscherne JS, Nurse K, Popienick P, Michel H, Sochacki M, Ofengand J (1999). "Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli." Biochemistry 38(6);1884-92. PMID: 10026269

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

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

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

Weitzmann91: Weitzmann C, Tumminia SJ, Boublik M, Ofengand J (1991). "A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of S7 is required for methylation of m2G966 and blocks methylation of m5C967 by their respective methyltransferases." Nucleic Acids Res 19(25);7089-95. PMID: 1766869


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, biocyc14.