2rns: Difference between revisions

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REFINEMENT OF THE CRYSTAL STRUCTURE OF RIBONUCLEASE S. COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE A STRUCTURES

OverviewOverview

Ribonuclease S (RNase-S) is a complex that consists of two proteolytic fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide (residues 1-20) and S-protein (residues 21-124). We have refined the crystal structures of three RNase-S complexes. The first two contain the full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5. The third one consists of a truncated form of S-peptide (residues 1-15) and was studied at pH 4.75 as the reference structure for a series of mutant peptide complexes to be reported separately. Excluding residues 16-23 which are either missing (in the S15 complex) or disordered (in both S20 complexes), all three structures refined at 1.6-A resolution are identical within the estimated errors in the coordinates (0.048 A for the backbone atoms). The R-values, residual error, range from 17.4% to 18.6%. The final model of S20, pH 4.75, includes 1 sulfate and 84 water molecules. The side chains of 11 residues were modeled in two discrete conformations. The final structures were independent of the particular RNase-A or RNase-S used as a starting model. An extensive comparison with refined crystal structures of RNase-A reveals that the core of the molecule which is held together with extensive hydrogen bonds is in identical pattern in all cases. However, the loop regions vary from one structure to another and are often characterized by high B-factors. The pattern of thermal parameters appears to be dependent on crystal packing and correlates well with the accessibility calculated in the crystal. Gln60 is a conserved residue in all sequences known to date for this class of ribonucleases. However, it is the only residue that is clearly defined in an unfavorable position (phi = -100 degrees, psi = -130 degrees) on the Ramachandran plot. The origin of the substantial differences between RNase-A and RNase-S in stability to both acid and temperature denaturation and in susceptibility to proteolysis at neutral pH is not obvious in our visual comparison of these two structures.

About this StructureAbout this Structure

2RNS is a Single protein structure of sequence from Bos taurus with as ligand. This structure supersedes the now removed PDB entry 1RNS. Active as Pancreatic ribonuclease, with EC number 3.1.27.5 Full crystallographic information is available from OCA.

ReferenceReference

Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures., Kim EE, Varadarajan R, Wyckoff HW, Richards FM, Biochemistry. 1992 Dec 15;31(49):12304-14. PMID:1463719

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-[[Image:2rns.jpg|left|200px]]<br /><applet load="2rns" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2rns.jpg|left|200px]]<br /><applet load="2rns" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2rns, resolution 1.6&Aring;" />
 '''REFINEMENT OF THE CRYSTAL STRUCTURE OF RIBONUCLEASE S. COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE A STRUCTURES'''<br />
 ==Overview==
-Ribonuclease S (RNase-S) is a complex that consists of two proteolytic, fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide, (residues 1-20) and S-protein (residues 21-124). We have refined the, crystal structures of three RNase-S complexes. The first two contain the, full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5., The third one consists of a truncated form of S-peptide (residues 1-15), and was studied at pH 4.75 as the reference structure for a series of, mutant peptide complexes to be reported separately. Excluding residues, 16-23 which are either missing (in the S15 complex) or disordered (in both, S20 complexes), all three structures refined at 1.6-A resolution are, identical within the estimated errors in the coordinates (0.048 A for the, backbone atoms). The R-values, residual error, range from 17.4% to 18.6%., The final model of S20, pH 4.75, includes 1 sulfate and 84 water, molecules. The side chains of 11 residues were modeled in two discrete, conformations. The final structures were independent of the particular, RNase-A or RNase-S used as a starting model. An extensive comparison with, refined crystal structures of RNase-A reveals that the core of the, molecule which is held together with extensive hydrogen bonds is in, identical pattern in all cases. However, the loop regions vary from one, structure to another and are often characterized by high B-factors. The, pattern of thermal parameters appears to be dependent on crystal packing, and correlates well with the accessibility calculated in the crystal., Gln60 is a conserved residue in all sequences known to date for this class, of ribonucleases. However, it is the only residue that is clearly defined, in an unfavorable position (phi = -100 degrees, psi = -130 degrees) on the, Ramachandran plot. The origin of the substantial differences between, RNase-A and RNase-S in stability to both acid and temperature denaturation, and in susceptibility to proteolysis at neutral pH is not obvious in our, visual comparison of these two structures.
+Ribonuclease S (RNase-S) is a complex that consists of two proteolytic fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide (residues 1-20) and S-protein (residues 21-124). We have refined the crystal structures of three RNase-S complexes. The first two contain the full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5. The third one consists of a truncated form of S-peptide (residues 1-15) and was studied at pH 4.75 as the reference structure for a series of mutant peptide complexes to be reported separately. Excluding residues 16-23 which are either missing (in the S15 complex) or disordered (in both S20 complexes), all three structures refined at 1.6-A resolution are identical within the estimated errors in the coordinates (0.048 A for the backbone atoms). The R-values, residual error, range from 17.4% to 18.6%. The final model of S20, pH 4.75, includes 1 sulfate and 84 water molecules. The side chains of 11 residues were modeled in two discrete conformations. The final structures were independent of the particular RNase-A or RNase-S used as a starting model. An extensive comparison with refined crystal structures of RNase-A reveals that the core of the molecule which is held together with extensive hydrogen bonds is in identical pattern in all cases. However, the loop regions vary from one structure to another and are often characterized by high B-factors. The pattern of thermal parameters appears to be dependent on crystal packing and correlates well with the accessibility calculated in the crystal. Gln60 is a conserved residue in all sequences known to date for this class of ribonucleases. However, it is the only residue that is clearly defined in an unfavorable position (phi = -100 degrees, psi = -130 degrees) on the Ramachandran plot. The origin of the substantial differences between RNase-A and RNase-S in stability to both acid and temperature denaturation and in susceptibility to proteolysis at neutral pH is not obvious in our visual comparison of these two structures.
 ==About this Structure==
-RNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1RNS. Active as [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2RNS OCA].
+RNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1RNS. Active as [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RNS OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Pancreatic ribonuclease]]
 [[Category: Single protein]]
-[[Category: Kim, E.E.]]
+[[Category: Kim, E E.]]
-[[Category: Richards, F.M.]]
+[[Category: Richards, F M.]]
 [[Category: Varadarajan, R.]]
-[[Category: Wyckoff, H.W.]]
+[[Category: Wyckoff, H W.]]
 [[Category: SO4]]
 [[Category: hydrolase(phosphoric diester]]
 [[Category: rna)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:58:20 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:48:40 2008''