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 with as ligand. Active as Ribonuclease T(1), with EC number 3.1.27.3 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

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-[[Image:1rds.gif|left|200px]]<br /><applet load="1rds" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1rds.gif|left|200px]]<br /><applet load="1rds" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1rds, resolution 1.8&Aring;" />
 '''CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE'''<br />
 ==Overview==
-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., &amp; 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., &amp;, 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.
+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., &amp; 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., &amp; 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 Structure==
-RDS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_phoenicis Aspergillus phoenicis] with GPC as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1RDS OCA].
+RDS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_phoenicis Aspergillus phoenicis] with <scene name='pdbligand=GPC:'>GPC</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1RDS OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Mitsui, Y.]]
-[[Category: Nakamura, K.T.]]
+[[Category: Nakamura, K T.]]
 [[Category: Nonaka, T.]]
 [[Category: GPC]]
 [[Category: hydrolase(endoribonuclease)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:30:19 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:46 2008''