2rnt: Difference between revisions
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|PDB= 2rnt |SIZE=350|CAPTION= <scene name='initialview01'>2rnt</scene>, resolution 1.8Å | |PDB= 2rnt |SIZE=350|CAPTION= <scene name='initialview01'>2rnt</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rnt OCA], [http://www.ebi.ac.uk/pdbsum/2rnt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2rnt RCSB]</span> | |||
}} | }} | ||
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[[Category: Maslowska, M.]] | [[Category: Maslowska, M.]] | ||
[[Category: Saenger, W.]] | [[Category: Saenger, W.]] | ||
[[Category: hydrolase(endoribonuclease)]] | [[Category: hydrolase(endoribonuclease)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:02:26 2008'' | ||
Revision as of 05:02, 31 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Ribonuclease T(1), with EC number 3.1.27.3 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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
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. 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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