PDBsum entry 3crm

Transferase

PDB id: 3crm

Contents

Protein chain

236 a.a. *

Waters ×109

* Residue conservation analysis

PDB id:

3crm

Name:

Transferase

Title:

Structure of tRNA dimethylallyltransferase: RNA modification through a channel

Structure:

tRNA delta(2)-isopentenylpyrophosphate transferase. Chain: a. Synonym: ipp transferase, isopentenyl-diphosphate:trna isopentenyltransferase, iptase, ippt, tRNA dmatase. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: miaa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.211 R-free: 0.230

Authors:

R.H.Huang,W.Xie,C.Zhou

Key ref:

W.Xie et al. (2007). Structure of tRNA dimethylallyltransferase: RNA modification through a channel. J Mol Biol, 367, 872-881. PubMed id: 17292915 DOI: 10.1016/j.jmb.2007.01.048

Date:

07-Apr-08 Release date: 29-Apr-08

Protein chain

Q9HUL9  (MIAA_PSEAE) -  tRNA dimethylallyltransferase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 323 a.a.

Struc: 236 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.5.1.75 - tRNA dimethylallyltransferase.
• Reaction: adenosine₃₇ in tRNA + dimethylallyl diphosphate = N₆- dimethylallyladenosine₃₇ in tRNA + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2007.01.048

J Mol Biol 367:872-881 (2007)

PubMed id: 17292915

Structure of tRNA dimethylallyltransferase: RNA modification through a channel.

W.Xie, C.Zhou, R.H.Huang.

ABSTRACT

Dimethylallyltransferase (DMATase) transfers a five-carbon isoprenoid moiety from dimethylallyl pyrophosphate (DMAPP) to the amino group of adenosine at position 37 of certain tRNAs. Reported here are the crystal structures of Pseudomonas aeruginosa DMATase alone and in complex with pyrophosphate at 1.9 A resolution. Surprisingly, the enzyme possesses a central channel spanning the entire width of the enzyme. Both the accepting substrate tRNA and the donating substrate DMAPP appear to enter the channel from opposite sides in an ordered sequence, with tRNA first and DMAPP second, and the RNA modification reaction occurs in the middle of the channel once the two substrates have met. The structure of DMATase is homologous to a class of small soluble kinases involved in biosynthesis of nucleotide precursors for nucleic acids, indicating its possibly evolutionary origin. Furthermore, specific recognition of the pyrophosphate by a conserved loop in DMATase, similar to the P-loop commonly seen in diverse nucleotide-binding proteins, demonstrates that DMATase is structurally and mechanistically distinct from farnesyltransferase, another family of prenyltransferases involved in protein modification.

Selected figure(s)

Figure 4.
Figure 4. Stereo view of C^α superposition of the DMATase structure with the three top scores from Dali structural homology search. DMATase is in blue, S. cerevisiae GMP kinase (PDB entry 1GKY, Z core = 12.1, rmsd = 2.9 Å) is in red, human UMP/CMP kinase (PDB entry 1TEV, Z core = 11.8, rmsd = 3.3 Å) is in magenta, and Leishmania major CMP kinase (PDB entry 1Y63, Z core = 10.9, rmsd = 3.2 Å) is in yellow. Figure 4. Stereo view of C^α superposition of the DMATase structure with the three top scores from Dali structural homology search. DMATase is in blue, S. cerevisiae GMP kinase (PDB entry 1GKY, Z core = 12.1, rmsd = 2.9 Å) is in red, human UMP/CMP kinase (PDB entry 1TEV, Z core = 11.8, rmsd = 3.3 Å) is in magenta, and Leishmania major CMP kinase (PDB entry 1Y63, Z core = 10.9, rmsd = 3.2 Å) is in yellow.

Figure 7.
Figure 7. Proposed mechanism of DMATase-catalyzed reaction. The tRNA substrate binds to the right side of channel and the base of A37 flips into the channel (step 1). DMAPP enters the channel from the left side and is stabilized by interacting with the P-loop as well as by coordinating with a Mg^2+ (step 2). Nucleophilic attack of the amino group in A37 on the DMA moiety of DMAPP results in the DMA moiety to be transferred from DMAPP to the A37 of tRNA, made possible by activation of the carbon atom directly linked to the pyrophosphate in DMAPP by the side-chains of T14 and R223, as well as deprotonation of the amino group in A37 with the side-chain of D37 (step 3). Figure 7. Proposed mechanism of DMATase-catalyzed reaction. The tRNA substrate binds to the right side of channel and the base of A37 flips into the channel (step 1). DMAPP enters the channel from the left side and is stabilized by interacting with the P-loop as well as by coordinating with a Mg^2+ (step 2). Nucleophilic attack of the amino group in A37 on the DMA moiety of DMAPP results in the DMA moiety to be transferred from DMAPP to the A37 of tRNA, made possible by activation of the carbon atom directly linked to the pyrophosphate in DMAPP by the side-chains of T14 and R223, as well as deprotonation of the amino group in A37 with the side-chain of D37 (step 3).

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 367, 872-881) copyright 2007.

Figures were selected by an automated process.