Structural analysis of 2qgn

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

Structure of Protein

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

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.

One domains ranges from residue 2-200 and residue 283-314. Another domain encompasses residues 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 5
Structural architecture of domain 1 signified by red regions in Figure 4.

Figure 6
Structural representation of domain 2 denoted by blue regions in Figure 4.

Ligand Binding Sites and Surface Clefts

Structural Alignment

Dali Output

PDB entry code for 2qgn was loaded onto DALI 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, 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 72ze5 superimposed against 2qgn via PyMOL.

Figure 83crm superimposed against 2qgn via PyMOL.

Figure 93crq superimposed against 2qgn via PyMOL.