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x * 42000, SDS-PAGE
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x * 38500, recombinant N-terminally His6-tagged enzyme, SDS-PAGE
dimer
may be the functional form
dimer
TrmD is an obligated homodimer that places each active site at the dimer interface
dimer
2 * 30586, calculated from sequence
dimer
each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain
dimer
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TrmD features a trefoil-knot active-site structure
dimer
deep-trefoil knot structure
dimer
TrmD is an obligated homodimer that places each active site at the dimer interface
dimer
deep-trefoil knot structure
dimer
TrmD is an obligated homodimer that places each active site at the dimer interface
dimer
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deep-trefoil knot structure
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dimer
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deep-trefoil knot structure
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dimer
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deep-trefoil knot structure
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dimer
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deep-trefoil knot structure
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dimer
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crystal structure analysis
dimer
enzyme TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer
dimer
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enzyme TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer
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dimer
TrmD is an obligated homodimer that places each active site at the dimer interface
dimer
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TrmD is an obligated homodimer that places each active site at the dimer interface
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dimer
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TrmD is an obligated homodimer that places each active site at the dimer interface
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homodimer
TrmD exists as an obligate homodimer, with each subunit featuring an N-terminal domain (residues 1-159), a flexible linker (residues 160-169), and a C-terminal domain (residues 170-250), the active site is built between the N-terminal domain of one subunit and the flexible linker and the C-terminal domain of the other
homodimer
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enzyme TrmD consists of the N-terminal domain (residues 1-160) and the C-terminal domain (residues 169-246), and the interdomain linker of residues 161-168 is disordered in the tRNA-free structures
homodimer
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enzyme TrmD consists of the N-terminal domain (residues 1-160) and the C-terminal domain (residues 169-246), and the interdomain linker of residues 161-168 is disordered in the tRNA-free structures
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homodimer
analysis of PaTrmD-SAM structure showing the dimer architecture and SAM-binding active site, overview
homodimer
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analysis of PaTrmD-SAM structure showing the dimer architecture and SAM-binding active site, overview
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monomer
1 * 60500, SDS-PAGE
monomer
Rossmann fold structure
monomer
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Rossmann fold structure
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monomer
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Rossmann fold structure
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monomer
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Rossmann fold structure
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monomer
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Rossmann fold structure
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monomer
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Rossmann fold structure
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monomer
Rossmann fold structure
monomer
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Rossmann fold structure
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additional information
knot structures, domain arrangements, subunit structures and reaction mechanisms of tRNA methyltransferases with a SPOUT fold, overview
additional information
without the knot, as found in the crystal structure of Aquifex aeolicus TrmD, AdoMet cannot bend and can only exist in the open shape. Without being in the bent shape, AdoMet is be positioned in a spatial geometry incompatible with the position of the G37 base and unfavorable for methyl transfer. The m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA
additional information
in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
additional information
knot structures, domain arrangements, subunit structures and reaction mechanisms of tRNA methyltransferases with a SPOUT fold, overview
additional information
enzyme structures of apo- and binary tRNA-free forms, and of ternary complex including AdoMet, molecular dynamic analysis, simulations and modelling, overview. Molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method
additional information
in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
additional information
knot structures, domain arrangements, subunit structures and reaction mechanisms of tRNA methyltransferases with a SPOUT fold, overview
additional information
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three-dimensional enzyme model, overview
additional information
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Trm5 features the Rossmann fold
additional information
backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
additional information
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backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
additional information
the PaTrmD monomer is formed by an N-terminal domain (NTD) that adopts a alpha/beta fold (residues 5-165) and a mostly helical C-terminal domain (CTD) spanning residues 178-250. These two domains are connected by a linker spanning residues 166-177 that acts as a lid covering up the active site
additional information
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the PaTrmD monomer is formed by an N-terminal domain (NTD) that adopts a alpha/beta fold (residues 5-165) and a mostly helical C-terminal domain (CTD) spanning residues 178-250. These two domains are connected by a linker spanning residues 166-177 that acts as a lid covering up the active site
additional information
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backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa and secondary structure analysis
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additional information
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the PaTrmD monomer is formed by an N-terminal domain (NTD) that adopts a alpha/beta fold (residues 5-165) and a mostly helical C-terminal domain (CTD) spanning residues 178-250. These two domains are connected by a linker spanning residues 166-177 that acts as a lid covering up the active site
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additional information
enzyme structure analysis, the 38.5-kDa protein is composed of three domains: D1 (M1-P60), D2 (N70-S162) and D3 (K163-S333) D1 and D2 are connected through an interdomain linker (M61-K69), overview
additional information
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enzyme structure analysis, the 38.5-kDa protein is composed of three domains: D1 (M1-P60), D2 (N70-S162) and D3 (K163-S333) D1 and D2 are connected through an interdomain linker (M61-K69), overview
additional information
substrate interactions with the catalytic region in the PaTrm5a-tRNAPhe-SAH ternary complex, overview
additional information
the PaTrm5b protein displays an open conformation
additional information
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the PaTrm5b protein displays an open conformation
additional information
in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
additional information
-
in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
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additional information
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in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
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