1dix: Difference between revisions

Revision as of 13:17, 21 February 2008

CRYSTAL STRUCTURE OF RNASE LE

OverviewOverview

Ribonuclease LE (RNase LE) from cultured tomato (Lycopersicon esculentum) cells is a member of the RNase T(2) family showing broad base specificity. The crystal structure of RNase LE has been determined at 1.65 A resolution. The structure consists of seven alpha-helices and seven beta-strands, belonging to an alpha+beta type structure. Comparison of the structure of RNase LE with that of RNase Rh, a microbial RNase belonging to the RNase T(2) family, reveals that while the overall folding topologies are similar to each other, major insertions and deletions are found at the N-terminal regions. The structural comparison, an amino acid sequence alignment of the RNase T(2) enzymes, and comparison of the disulfide-bonding pattern of these enzymes show that the structure of RNase LE shown here is the basic framework of the animal/plant subfamily of RNase T(2) enzymes (including a self-incompatibility protein called S-RNase), and the structure of RNase Rh is that of the fungal subfamily of RNase T(2) enzymes (including RNase T(2)). Subsequently, we superposed the active-site of the RNase LE with that of RNase Rh and found that (1) His39, Trp42, His92, Glu93, Lys96, and His97 of RNase LE coincided exactly with His46, Trp49, His104, Glu105, Lys108, and His109, respectively, of RNase Rh, and (2) two conserved water molecules were found at the putative P(1) sites of both enzymes. These facts suggest that plant RNase LE has a very similar hydrolysis mechanism to that of fungal RNase Rh, and almost all the RNase T(2) enzymes widely distributed in various species share a common catalytic mechanism. A cluster of hydrophobic residues was found on the active-site face of the RNase LE molecule and two large hydrophobic pockets exist. These hydrophobic pockets appear to be base binding sites mainly by hydrophobic interactions and are responsible for the base non-specificity of RNase LE.

About this StructureAbout this Structure

1DIX is a Single protein structure of sequence from Solanum lycopersicum. Active as Ribonuclease T(2), with EC number 3.1.27.1 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of a plant ribonuclease, RNase LE., Tanaka N, Arai J, Inokuchi N, Koyama T, Ohgi K, Irie M, Nakamura KT, J Mol Biol. 2000 May 19;298(5):859-73. PMID:10801354

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-[[Image:1dix.jpg|left|200px]]<br /><applet load="1dix" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dix.jpg|left|200px]]<br /><applet load="1dix" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dix, resolution 1.65&Aring;" />
 '''CRYSTAL STRUCTURE OF RNASE LE'''<br />
 ==Overview==
-Ribonuclease LE (RNase LE) from cultured tomato (Lycopersicon esculentum), cells is a member of the RNase T(2) family showing broad base specificity., The crystal structure of RNase LE has been determined at 1.65 A, resolution. The structure consists of seven alpha-helices and seven, beta-strands, belonging to an alpha+beta type structure. Comparison of the, structure of RNase LE with that of RNase Rh, a microbial RNase belonging, to the RNase T(2) family, reveals that while the overall folding, topologies are similar to each other, major insertions and deletions are, found at the N-terminal regions. The structural comparison, an amino acid, sequence alignment of the RNase T(2) enzymes, and comparison of the, disulfide-bonding pattern of these enzymes show that the structure of, RNase LE shown here is the basic framework of the animal/plant subfamily, of RNase T(2) enzymes (including a self-incompatibility protein called, S-RNase), and the structure of RNase Rh is that of the fungal subfamily of, RNase T(2) enzymes (including RNase T(2)). Subsequently, we superposed the, active-site of the RNase LE with that of RNase Rh and found that (1), His39, Trp42, His92, Glu93, Lys96, and His97 of RNase LE coincided exactly, with His46, Trp49, His104, Glu105, Lys108, and His109, respectively, of, RNase Rh, and (2) two conserved water molecules were found at the putative, P(1) sites of both enzymes. These facts suggest that plant RNase LE has a, very similar hydrolysis mechanism to that of fungal RNase Rh, and almost, all the RNase T(2) enzymes widely distributed in various species share a, common catalytic mechanism. A cluster of hydrophobic residues was found on, the active-site face of the RNase LE molecule and two large hydrophobic, pockets exist. These hydrophobic pockets appear to be base binding sites, mainly by hydrophobic interactions and are responsible for the base, non-specificity of RNase LE.
+Ribonuclease LE (RNase LE) from cultured tomato (Lycopersicon esculentum) cells is a member of the RNase T(2) family showing broad base specificity. The crystal structure of RNase LE has been determined at 1.65 A resolution. The structure consists of seven alpha-helices and seven beta-strands, belonging to an alpha+beta type structure. Comparison of the structure of RNase LE with that of RNase Rh, a microbial RNase belonging to the RNase T(2) family, reveals that while the overall folding topologies are similar to each other, major insertions and deletions are found at the N-terminal regions. The structural comparison, an amino acid sequence alignment of the RNase T(2) enzymes, and comparison of the disulfide-bonding pattern of these enzymes show that the structure of RNase LE shown here is the basic framework of the animal/plant subfamily of RNase T(2) enzymes (including a self-incompatibility protein called S-RNase), and the structure of RNase Rh is that of the fungal subfamily of RNase T(2) enzymes (including RNase T(2)). Subsequently, we superposed the active-site of the RNase LE with that of RNase Rh and found that (1) His39, Trp42, His92, Glu93, Lys96, and His97 of RNase LE coincided exactly with His46, Trp49, His104, Glu105, Lys108, and His109, respectively, of RNase Rh, and (2) two conserved water molecules were found at the putative P(1) sites of both enzymes. These facts suggest that plant RNase LE has a very similar hydrolysis mechanism to that of fungal RNase Rh, and almost all the RNase T(2) enzymes widely distributed in various species share a common catalytic mechanism. A cluster of hydrophobic residues was found on the active-site face of the RNase LE molecule and two large hydrophobic pockets exist. These hydrophobic pockets appear to be base binding sites mainly by hydrophobic interactions and are responsible for the base non-specificity of RNase LE.
 ==About this Structure==
-DIX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(2) Ribonuclease T(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.1 3.1.27.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DIX OCA].
+DIX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(2) Ribonuclease T(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.1 3.1.27.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIX OCA].
 ==Reference==
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 [[Category: Single protein]]
 [[Category: Solanum lycopersicum]]
-[[Category: Nakamura, K.T.]]
+[[Category: Nakamura, K T.]]
 [[Category: Tanaka, N.]]
 [[Category: alpha plus beta]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:18:54 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:01 2008''