1rds: Difference between revisions

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CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE

OverviewOverview

A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus saitoi, has been crystallized as a complex with a substrate analogue GfpC where the 2'-hydroxyl (2'-OH) group of guanosine in guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom to prevent transesterification. The crystal structure of the complex was solved at 1.8-A resolution to a final R-factor of 0.204. The role of His92 (RNase T1 numbering) as the general acid catalyst was confirmed. Of the two alternative candidates for a general base to abstract a proton from the 2'-OH group, His40 and Glu58 were found close to the 2'-F atom, making the decision between the two groups difficult. We then superposed the active site of the RNase Ms/GfpC complex with that of pancreatic ribonuclease S (RNase S) complexed with a substrate analogue UpcA, a phosphonate analogue of uridylyl-3',5'-adenosine (UpA), and found that His12 and His119 of RNase A almost exactly coincided with Glu58 and His92, respectively, of RNase Ms. Similar superposition with a prokaryotic microbial ribonuclease, RNase St [Nakamura, K. T., Iwahashi, K., Yamamoto, Y., Iitaka, Y., Yoshida, N., & Mitsui, Y. (1982) Nature 299, 564-566], also indicated Glu58 as a general base. Thus the present comparative geometrical studies consistently favor, albeit indirectly, the traditional as well as the most recent notion [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072] that Glu58, rather than His40, must be the general base catalyst in the intact enzymes of the RNase T1 family.

About this StructureAbout this Structure

1RDS is a Single protein structure of sequence from Aspergillus phoenicis. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue., Nonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y, Biochemistry. 1993 Nov 9;32(44):11825-37. PMID:8218254 Page seeded by OCA on Sat May 3 07:22:21 2008

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OCA

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 [[Image:1rds.gif|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_1rds", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=GPC:2&#39;-FLUOROGUANYLYL-(3&#39;-5&#39;)-PHOSPHOCYTIDINE'>GPC</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
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-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rds OCA], [http://www.ebi.ac.uk/pdbsum/1rds PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rds RCSB]</span>
-}}
 '''CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE'''
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 Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue., Nonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y, Biochemistry. 1993 Nov 9;32(44):11825-37. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8218254 8218254]
 [[Category: Aspergillus phoenicis]]
-[[Category: Ribonuclease T(1)]]
 [[Category: Single protein]]
 [[Category: Mitsui, Y.]]
 [[Category: Nakamura, K T.]]
 [[Category: Nonaka, T.]]
-[[Category: hydrolase(endoribonuclease)]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:22:21 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:42 2008''