Results - 2gqnA

Structure of tRNA isopentenyltransferase

Protein Sequence in FASTA format

>gi|152149497|pdb|2QGN|A Chain A, Crystal Structure Of Trna Isopentenylpyrophosphate Transferase (Bh2366) From Bacillus Halodurans, Northeast Structural Genomics Consortium Target Bhr41. XKEKLVAIVGPTAVGKTKTSVXLAKRLNGEVISGDSXQVYRGXDIGTAKITAEEXDGVPHHLIDIKDPSE SFSVADFQDLATPLITEIHERGRLPFLVGGTGLYVNAVIHQFNLGDIRADEDYRHELEAFVNSYGVQALH DKLSKIDPKAAAAIHPNNYRRVIRALEIIKLTGKTVTEQARHEEETPSPYNLVXIGLTXERDVLYDRINR RVDQXVEEGLIDEAKKLYDRGIRDCQSVQAIGYKEXYDYLDGNVTLEEAIDTLKRNSRRYAKRQLTWFRN KANVTWFDXTDVDFDKKIXEIHNFIAGKLEEKSKLEHHHHHH

Protein Structure

Figure 1
Structure of TRNA isopentenyl transferase 1 showing helix, sheet and loop. Image constructed from PyMOL.

Secondary Structure

Analysis of the secondary structure acquired from Protein Data Bank showed results as displayed below :

Surface Properties of 2qgn

Figure 2
Surface property displayed by 2qgn. Red colour indicates negatively charged regions, while blue colour indicates positively charged regions.

Domains

2qgnA is composed of two main domains. CATH analysis of 2qgn resulted in the finding of two main domains composing 2qgnA.

Domain 1 ranges from residue 2-200 and residue 283-314. Domain 2 encompasses residues stretching from 201-282.

Figure 4
Two main domains exhibited by tRNA isopentenyl transferase(2qgnA). Blue regions denote first domain while Red regions underlies second domain.

Figure 5Ribbon structure of domain 2 signified by red regions in Figure 4.

Figure 6Structural representation of domain 1 denoted by blue regions in Figure 4.

Ligand Binding Sites and Surface Clefts

Protein-ligand interaction

Hydrophillic binding sites

File:Hydrophillic.jpg

Bridged-H-bond binding sites

File:H-bond.jpg

Hydrophobic binding sites

File:Hydrophobic.jpg

Conserved residues for tRNA isopentenyl transferase from Clustal alignment

Multiple sequence alignment from ClustalX allowed conserved regions in 2qgn and related species to be found.

Figure 5 Conserved regions among various species were shown in red, with their respective residues labelled. Yellow sphere shows the location of the ligand. Image was constructed from PyMOL.

Structural Alignment

Profunc

Related protein sequences

Proteins with similar fold retrived from SSM (Secondary Structure Matching)

Dali Output

PDB entry code for 2qgn was loaded onto DALI server to search for structurally similar neighbours. Displayed below are the results from DALI search :-

A total of 527 hits were found from DALI search, nonetheless only the first 20 hits that may be of significance were shown on the figure. Based on the outcome of DALI and Profunc, PDB files of each structurally similar protein was obtained from PDB. These were each superimposed against 2qgn using the PyMOL software, to compare the structural similiarity. Results are as below :

Figure 7 3crq superimposed against 2qgn via PyMOL. 2qgn indicated in green.

Figure 8 3crm superimposed against 2qgn via PyMOL. 2qgn indicated in green.

Figure 9 2ze7 superimposed against 2qgn via PyMOL. 2qgn indicated in green.

Figure 10 2qor superimposed against 2qgn via PyMOL. 2qgn indicated in green

As indicated by the figures above, each structures were structurally similar to 2qgn, suggesting that they could have functionally similar properties. Nonetheless,notice that 2-qor is only partially similar to 2qgn structure. As the Z-score decreases for the DALI output, the structural similarity decreases as well. For this reason, functional analysis of 2qgn was only done for DALI outputs with lali scores higher than 200.

Localisation Expression of tRNA isopentenyltransferase

Generally, this enzyme is expressed in all tissue types since it is important that functional protein are synthesized in each of these tissues. Specifically, it is highly expressed in adipose tissues as well as oocytes. Relatively high amounts of this enzyme is expressed in prostate, adrenal gland, B-cells and trachea. The reason why tRNA-IPT are at higher concentrations in these tissues may reflect higher levels of protein synthesis.