1vdx
From Proteopedia
(New page: 200px<br /><applet load="1vdx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vdx, resolution 2.40Å" /> '''Crystal Structure of...) |
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| - | [[Image:1vdx.gif|left|200px]]<br /><applet load="1vdx" size=" | + | [[Image:1vdx.gif|left|200px]]<br /><applet load="1vdx" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1vdx, resolution 2.40Å" /> | caption="1vdx, resolution 2.40Å" /> | ||
'''Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase'''<br /> | '''Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily | + | Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter. |
==About this Structure== | ==About this Structure== | ||
| - | 1VDX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with CL as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] Full crystallographic information is available from [http:// | + | 1VDX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/RNA_ligase_(ATP) RNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.3 6.5.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDX OCA]. |
==Reference== | ==Reference== | ||
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[[Category: RNA ligase (ATP)]] | [[Category: RNA ligase (ATP)]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
| - | [[Category: Rehse, P | + | [[Category: Rehse, P H.]] |
| - | [[Category: Tahirov, T | + | [[Category: Tahirov, T H.]] |
[[Category: CL]] | [[Category: CL]] | ||
[[Category: ligase]] | [[Category: ligase]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:34:15 2008'' |
Revision as of 13:34, 21 February 2008
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Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase
Overview
Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter.
About this Structure
1VDX is a Single protein structure of sequence from Pyrococcus horikoshii with as ligand. Active as RNA ligase (ATP), with EC number 6.5.1.3 Full crystallographic information is available from OCA.
Reference
Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii., Rehse PH, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1207-12. Epub 2005, Aug 16. PMID:16131753
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Categories: Pyrococcus horikoshii | RNA ligase (ATP) | Single protein | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Rehse, P H. | Tahirov, T H. | CL | Ligase | National project on protein structural and functional analyses | Nppsfa | Riken structural genomics/proteomics initiative | Rsgi | Structural genomics
