2rnt
From Proteopedia
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| - | [[Image:2rnt.jpg|left|200px]] | + | [[Image:2rnt.jpg|left|200px]] |
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| - | '''THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION''' | + | {{Structure |
| + | |PDB= 2rnt |SIZE=350|CAPTION= <scene name='initialview01'>2rnt</scene>, resolution 1.8Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=GPG:GUANYLYL-2',5'-PHOSPHOGUANOSINE'>GPG</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2RNT is a [ | + | 2RNT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNT OCA]. |
==Reference== | ==Reference== | ||
| - | Three-dimensional structure of ribonuclease T1 complexed with guanylyl-2',5'-guanosine at 1.8 A resolution., Koepke J, Maslowska M, Heinemann U, Saenger W, J Mol Biol. 1989 Apr 5;206(3):475-88. PMID:[http:// | + | Three-dimensional structure of ribonuclease T1 complexed with guanylyl-2',5'-guanosine at 1.8 A resolution., Koepke J, Maslowska M, Heinemann U, Saenger W, J Mol Biol. 1989 Apr 5;206(3):475-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2541256 2541256] |
[[Category: Aspergillus oryzae]] | [[Category: Aspergillus oryzae]] | ||
[[Category: Ribonuclease T(1)]] | [[Category: Ribonuclease T(1)]] | ||
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[[Category: hydrolase(endoribonuclease)]] | [[Category: hydrolase(endoribonuclease)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:37:48 2008'' |
Revision as of 16:37, 20 March 2008
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| , resolution 1.8Å | |||||||
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| Ligands: | and | ||||||
| Activity: | Ribonuclease T(1), with EC number 3.1.27.3 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION
Overview
The enzyme ribonuclease T1 (RNase T1) isolated from Aspergillus oryzae was cocrystallized with the specific inhibitor guanylyl-2',5'-guanosine (2',5'-GpG) and the structure refined by the stereochemically restrained least-squares refinement method to a crystallographic R-factor of 14.9% for X-ray data above 3 sigma in the resolution range 6 to 1.8 A. The refined model consists of 781 protein atoms, 43 inhibitor atoms in a major site and 29 inhibitor atoms in a minor site, 107 water oxygen atoms, and a metal site assigned as Ca. At the end of the refinement, the orientation of His, Asn and Gln side-chains was reinterpreted on the basis of two-dimensional nuclear magnetic resonance data. The crystal packing and enzyme conformation of the RNase T1/2',5'-GpG complex and of the near-isomorphous RNase T1/2'-GMP complex are comparable. The root-mean-square deviation is 0.73 A between equivalent protein atoms. Differences in the unit cell dimensions are mainly due to the bound inhibitor. The 5'-terminal guanine of 2',5'-GpG binds to RNase T1 in much the same way as in the 2'-GMP complex. In contrast, the hydrogen bonds between the catalytic center and the phosphate group are different and the 3'-terminal guanine forms no hydrogen bonds with the enzyme. This poor binding is reflected in a 2-fold disorder of 2',5'-GpG (except the 5'-terminal guanine), which originates from differences in the pucker of the 5'-terminal ribose. The pucker is C2'-exo for the major site (2/3 occupancy) and C1'-endo for the minor site (1/3 occupancy). The orientation of the major site is stabilized through stacking interactions between the 3'-terminal guanine and His92, an amino acid necessary for catalysis. This might explain the high inhibition rate observed for 2',5'-GpG, which exceeds that of all other inhibitors of type 2',5'-GpN. On the basis of distance criteria, one solvent peak in the electron density was identified as metal ion, probably Ca2+. The ion is co-ordinated by the two Asp15 carboxylate oxygen atoms and by six water molecules. The co-ordination polyhedron displays approximate 4m2 symmetry.
About this Structure
2RNT is a Single protein structure of sequence from Aspergillus oryzae. Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of ribonuclease T1 complexed with guanylyl-2',5'-guanosine at 1.8 A resolution., Koepke J, Maslowska M, Heinemann U, Saenger W, J Mol Biol. 1989 Apr 5;206(3):475-88. PMID:2541256
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