1rnb: Difference between revisions

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CRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS RESOLUTION

OverviewOverview

The ribonuclease excreted by Bacillus amyloliquefaciens, Barnase, was co-crystallized with the deoxy-dinucleotide d(GpC). The crystal structure was determined by molecular replacement from a model of free Barnase previously derived by Mauguen et al. Refinement was carried out using data to 1.9 A resolution. The final model, which has a crystallographic R factor of 22%, includes 869 protein atoms, 38 atoms from d(GpC), a sulfate ion and 73 water molecules. Only minor differences from free Barnase are seen in the protein moiety, the root-mean-square C alpha movement being 0.45 A. The dinucleotide has a folded conformation. It is located near the active site of the enzyme, but outside the protein molecule and making crystal packing contacts with neighboring molecules. The guanine base is stacked on the imidazole ring of active site His102, rather than binding to the so-called recognition loop as it does in other complexes of guanine nucleotides with microbial nucleases. The deoxyguanosine is syn, with the sugar ring in C-2'-endo conformation; the deoxycytidine is anti and C-4'-exo. In addition to the stacking interaction, His102 hydrogen bonds to the free 5' hydroxyl, which is located near the position where the 3' phosphate group is found in other inhibitors of microbial ribonucleases. While the mode of binding observed with d(GpC) and Barnase would be non-productive for a dinucleotide substrate, it may define a site for the nucleotide product on the 3' side of the hydrolyzed bond.

About this StructureAbout this Structure

1RNB is a Single protein structure of sequence from Bacillus amyloliquefaciens with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution., Baudet S, Janin J, J Mol Biol. 1991 May 5;219(1):123-32. PMID:2023257

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-[[Image:1rnb.gif|left|200px]]<br /><applet load="1rnb" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1rnb.gif|left|200px]]<br /><applet load="1rnb" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1rnb, resolution 1.9&Aring;" />
 '''CRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS RESOLUTION'''<br />
 ==Overview==
-The ribonuclease excreted by Bacillus amyloliquefaciens, Barnase, was, co-crystallized with the deoxy-dinucleotide d(GpC). The crystal structure, was determined by molecular replacement from a model of free Barnase, previously derived by Mauguen et al. Refinement was carried out using data, to 1.9 A resolution. The final model, which has a crystallographic R, factor of 22%, includes 869 protein atoms, 38 atoms from d(GpC), a sulfate, ion and 73 water molecules. Only minor differences from free Barnase are, seen in the protein moiety, the root-mean-square C alpha movement being, 0.45 A. The dinucleotide has a folded conformation. It is located near the, active site of the enzyme, but outside the protein molecule and making, crystal packing contacts with neighboring molecules. The guanine base is, stacked on the imidazole ring of active site His102, rather than binding, to the so-called recognition loop as it does in other complexes of guanine, nucleotides with microbial nucleases. The deoxyguanosine is syn, with the, sugar ring in C-2'-endo conformation; the deoxycytidine is anti and, C-4'-exo. In addition to the stacking interaction, His102 hydrogen bonds, to the free 5' hydroxyl, which is located near the position where the 3', phosphate group is found in other inhibitors of microbial ribonucleases., While the mode of binding observed with d(GpC) and Barnase would be, non-productive for a dinucleotide substrate, it may define a site for the, nucleotide product on the 3' side of the hydrolyzed bond.
+The ribonuclease excreted by Bacillus amyloliquefaciens, Barnase, was co-crystallized with the deoxy-dinucleotide d(GpC). The crystal structure was determined by molecular replacement from a model of free Barnase previously derived by Mauguen et al. Refinement was carried out using data to 1.9 A resolution. The final model, which has a crystallographic R factor of 22%, includes 869 protein atoms, 38 atoms from d(GpC), a sulfate ion and 73 water molecules. Only minor differences from free Barnase are seen in the protein moiety, the root-mean-square C alpha movement being 0.45 A. The dinucleotide has a folded conformation. It is located near the active site of the enzyme, but outside the protein molecule and making crystal packing contacts with neighboring molecules. The guanine base is stacked on the imidazole ring of active site His102, rather than binding to the so-called recognition loop as it does in other complexes of guanine nucleotides with microbial nucleases. The deoxyguanosine is syn, with the sugar ring in C-2'-endo conformation; the deoxycytidine is anti and C-4'-exo. In addition to the stacking interaction, His102 hydrogen bonds to the free 5' hydroxyl, which is located near the position where the 3' phosphate group is found in other inhibitors of microbial ribonucleases. While the mode of binding observed with d(GpC) and Barnase would be non-productive for a dinucleotide substrate, it may define a site for the nucleotide product on the 3' side of the hydrolyzed bond.
 ==About this Structure==
-RNB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RNB OCA].
+RNB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RNB OCA].
 ==Reference==
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 [[Category: endonuclease]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:43:39 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:38 2008''