4rsd
From Proteopedia
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| - | [[Image:4rsd.jpg|left|200px]]<br /><applet load="4rsd" size=" | + | [[Image:4rsd.jpg|left|200px]]<br /><applet load="4rsd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="4rsd, resolution 1.6Å" /> | caption="4rsd, resolution 1.6Å" /> | ||
'''STRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A'''<br /> | '''STRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 4RSD 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 ACT and CL as [http://en.wikipedia.org/wiki/ligands ligands]. 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] Known structural/functional Sites: <scene name='pdbsite=B1:Pyrimidine Binding Site On 5' Side Of Scissile Phosphate'>B1</scene>, <scene name='pdbsite=B2:Purine Binding Site On 3' Side Of Scissile Phosphate'>B2</scene>, <scene name='pdbsite=P1:Catalyzes Cleavage Of P-O5' Bond Of A Phosphoryl Group I ...'>P1</scene> and <scene name='pdbsite=P2:Phosphate Binding Site'>P2</scene>. Full crystallographic information is available from [http:// | + | 4RSD 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=ACT:'>ACT</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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] Known structural/functional Sites: <scene name='pdbsite=B1:Pyrimidine+Binding+Site+On+5'+Side+Of+Scissile+Phosphate'>B1</scene>, <scene name='pdbsite=B2:Purine+Binding+Site+On+3'+Side+Of+Scissile+Phosphate'>B2</scene>, <scene name='pdbsite=P1:Catalyzes+Cleavage+Of+P-O5'+Bond+Of+A+Phosphoryl+Group+I+...'>P1</scene> and <scene name='pdbsite=P2:Phosphate+Binding+Site'>P2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RSD OCA]. |
==Reference== | ==Reference== | ||
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[[Category: x-ray diffraction]] | [[Category: x-ray diffraction]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:53:10 2008'' |
Revision as of 08:53, 3 February 2008
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STRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A
Overview
The side chains of histidine and aspartate residues form a hydrogen bond, in the active sites of many enzymes. In serine proteases, the His...Asp, hydrogen bond of the catalytic triad is known to contribute greatly to, catalysis, perhaps via the formation of a low-barrier hydrogen bond. In, bovine pancreatic ribonuclease A (RNase A), the His...Asp dyad is composed, of His119 and Asp121. Previously, site-directed mutagenesis was used to, show that His119 has a fundamental role, to act as an acid during, catalysis of RNA cleavage [Thompson, J. E., and Raines, R. T. (1994) J., Am. Chem. Soc. 116, 5467-5468]. Here, Asp121 was replaced with an, asparagine or alanine residue. The crystalline structures of the two, variants were determined by X-ray diffraction analysis to a resolution of, 1.6 A with an R-factor of 0.18. Replacing Asp121 with an asparagine or, alanine residue does not perturb the overall conformation of the enzyme., In the structure of D121N RNase A, Ndelta rather than Odelta of Asn121, faces His119. This alignment in the crystalline state is unlikely to exist, in solution because catalysis by the D121N variant is not compromised, severely. The steady-state kinetic parameters for catalysis by the, wild-type and variant enzymes were determined for the cleavage of, uridylyl(3'-->5')adenosine and poly(cytidylic acid), and for the, hydrolysis of uridine 2',3'-cyclic phosphate. Replacing Asp121 decreases, the values of kcat/Km and kcat for cleavage by 10-fold (D121N) and, 10(2)-fold (D121A). Replacing Asp121 also decreases the values of kcat/Km, and kcat for hydrolysis by 10(0. 5)-fold (D121N) and 10-fold (D121A) but, has no other effect on the pH-rate profiles for hydrolysis. There is no, evidence for the formation of a low-barrier hydrogen bond between His119, and either an aspartate or an asparagine residue at position 121., Apparently, the major role of Asp121 is to orient the proper tautomer of, His119 for catalysis. Thus, the mere presence of a His...Asp dyad in an, enzymic active site is not a mandate for its being crucial in effecting, catalysis.
About this Structure
4RSD is a Single protein structure of sequence from Bos taurus with and as ligands. Active as Pancreatic ribonuclease, with EC number 3.1.27.5 Known structural/functional Sites: , , and . Full crystallographic information is available from OCA.
Reference
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes., Schultz LW, Quirk DJ, Raines RT, Biochemistry. 1998 Jun 23;37(25):8886-98. PMID:9636030
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