2rnt: Difference between revisions

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THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION

OverviewOverview

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 StructureAbout this Structure

2RNT is a Single protein structure of sequence from Aspergillus oryzae with and as ligands. Active as Ribonuclease T(1), with EC number 3.1.27.3 Full crystallographic information is available from OCA.

ReferenceReference

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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-[[Image:2rnt.jpg|left|200px]]<br /><applet load="2rnt" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2rnt.jpg|left|200px]]<br /><applet load="2rnt" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2rnt, resolution 1.8&Aring;" />
 '''THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE T1 COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE AT 1.8 ANGSTROMS RESOLUTION'''<br />
 ==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.
+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==
-RNT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with CA and GPG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2RNT OCA].
+RNT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=GPG:'>GPG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNT OCA].
 ==Reference==
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 [[Category: hydrolase(endoribonuclease)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:58:25 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:48:43 2008''