BRENDA - Enzyme Database show
show all sequences of 2.1.1.193

Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m3U1498) from crystal and solution structures

Zhang, H.; Wan, H.; Gao, Z.Q.; Wei, Y.; Wang, W.J.; Liu, G.F.; Shtykova, E.V.; Xu, J.H.; Dong, Y.H.; J. Mol. Biol. 423, 576-589 (2012)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
sitting drop vapor diffusion method at room temperature, 0.15 M potassium thiocyanate and 24% w/v PEG monomethyl ether 2000, 3-4 days, crystal soaking in S-adenosyl-L-methionine solution or cocrystallization of enzyme and cofactor are not successful, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement
Escherichia coli
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
thermodynamics of S-adenosyl-L-methionine binding by RsmE, thermodynamic analysis, overview
Escherichia coli
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
Escherichia coli
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P0AGL7
gene rsmE
-
Reaction
Reaction
Commentary
Organism
S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
structure-function relationship and catalytic mechanism, overview
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
-
720262
Escherichia coli
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
720262
Escherichia coli
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
-
?
Subunits
Subunits
Commentary
Organism
homodimer
the crystal structure in monomer shows that RsmE consists of two distinct but structurally related domains: the pseudouridine synthases and archaeosine-specific transglycosylasess-like RNA recognition and binding domain, PUA, and the conserved MTase domain with a deep trefoil knot
Escherichia coli
More
the methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY. Structural comparisons of N-terminal and C-terminal domains of RsmE with related proteins, overview
Escherichia coli
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
one molecule bound per subunit of the enzyme homodimer
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
one molecule bound per subunit of the enzyme homodimer
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
sitting drop vapor diffusion method at room temperature, 0.15 M potassium thiocyanate and 24% w/v PEG monomethyl ether 2000, 3-4 days, crystal soaking in S-adenosyl-L-methionine solution or cocrystallization of enzyme and cofactor are not successful, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement
Escherichia coli
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
thermodynamics of S-adenosyl-L-methionine binding by RsmE, thermodynamic analysis, overview
Escherichia coli
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
Escherichia coli
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
-
720262
Escherichia coli
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
720262
Escherichia coli
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
the crystal structure in monomer shows that RsmE consists of two distinct but structurally related domains: the pseudouridine synthases and archaeosine-specific transglycosylasess-like RNA recognition and binding domain, PUA, and the conserved MTase domain with a deep trefoil knot
Escherichia coli
More
the methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY. Structural comparisons of N-terminal and C-terminal domains of RsmE with related proteins, overview
Escherichia coli
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
General Information
General Information
Commentary
Organism
evolution
RsmE is the founding member of a RNA methyltransferase family responsible for N3-methylation of U1498 in 16S ribosomal RNA. It is well conserved across bacteria and plants and may play an 30 important role in ribosomal intersubunit communication
Escherichia coli
additional information
RsmE forms a flexible dimeric conformation that is essential for substrate binding. RsmE-S-adenosyl-L-methionine-uridylic acid complex modeling and substrate binding structure, overview. The MTase domain of one subunit in dimeric RsmE is responsible for binding of one S-adenosyl-L-methionine molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule, the ribosomal RNA fragment and ribosomal protein complex. The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY
Escherichia coli
physiological function
RsmE is responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
evolution
RsmE is the founding member of a RNA methyltransferase family responsible for N3-methylation of U1498 in 16S ribosomal RNA. It is well conserved across bacteria and plants and may play an 30 important role in ribosomal intersubunit communication
Escherichia coli
additional information
RsmE forms a flexible dimeric conformation that is essential for substrate binding. RsmE-S-adenosyl-L-methionine-uridylic acid complex modeling and substrate binding structure, overview. The MTase domain of one subunit in dimeric RsmE is responsible for binding of one S-adenosyl-L-methionine molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule, the ribosomal RNA fragment and ribosomal protein complex. The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY
Escherichia coli
physiological function
RsmE is responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli
Escherichia coli
Other publictions for EC 2.1.1.193
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
733010
Kumar
The structure of Rv2372c ident ...
Mycobacterium tuberculosis
Acta Crystallogr. Sect. D
70
821-832
2014
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1
1
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1
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3
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1
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1
1
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1
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1
1
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1
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1
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1
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735238
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1
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1
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1
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1
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1
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720262
Zhang
Insights into the catalytic me ...
Escherichia coli
J. Mol. Biol.
423
576-589
2012
-
-
-
1
-
-
-
1
-
1
-
1
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1
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1
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2
2
1
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1
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1
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1
1
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1
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1
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1
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-
-
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2
2
1
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1
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3
3
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-
706717
Basturea
Substrate specificity and prop ...
Escherichia coli
RNA
13
1969-1976
2007
1
-
-
-
-
-
1
2
-
2
1
1
-
1
-
-
-
-
-
-
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2
1
1
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2
1
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1
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1
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2
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2
1
1
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2
1
1
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2
1
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706714
Basturea
Identification and characteriz ...
Escherichia coli
RNA
12
426-434
2006
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1
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-
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1
1
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3
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1
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2
1
1
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1
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1
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1
1
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1
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2
1
1
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1
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1
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