1bir

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|PDB= 1bir |SIZE=350|CAPTION= <scene name='initialview01'>1bir</scene>, resolution 1.8&Aring;
|PDB= 1bir |SIZE=350|CAPTION= <scene name='initialview01'>1bir</scene>, resolution 1.8&Aring;
|SITE=
|SITE=
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=2GP:GUANOSINE-2'-MONOPHOSPHATE'>2GP</scene>
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=2GP:GUANOSINE-2&#39;-MONOPHOSPHATE'>2GP</scene>
|ACTIVITY= [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]
|ACTIVITY= [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]
|GENE= SYNTHETIC GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5062 Aspergillus oryzae])
|GENE= SYNTHETIC GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5062 Aspergillus oryzae])
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[[Category: nuclease]]
[[Category: nuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:11:35 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 11:15:27 2008''

Revision as of 09:15, 23 March 2008

Image:1bir.jpg


PDB ID 1bir

Drag the structure with the mouse to rotate
, resolution 1.8Å
Ligands: and
Gene: SYNTHETIC GENE (Aspergillus oryzae)
Activity: Ribonuclease T(1), with EC number 3.1.27.3
Coordinates: save as pdb, mmCIF, xml



RIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP


Overview

The function of the conserved Phe 100 residue of RNase T1 (EC 3.1.27.3) has been investigated by site-directed mutagenesis and X-ray crystallography. Replacement of Phe 100 by alanine results in a mutant enzyme with kcat reduced 75-fold and a small increase in Km for the dinucleoside phosphate substrate GpC. The Phe 100 Ala substitution has similar effects on the turnover rates of GpC and its minimal analogue GpOMe, in which the leaving cytidine is replaced by methanol. The contribution to catalysis is independent of the nature of the leaving group, indicating that Phe 100 belongs to the primary site. The contribution of Phe 100 to catalysis may result from a direct van der Waals contact between its aromatic ring and the phosphate moiety of the substrate. Phe 100 may also contribute to the positioning of the pentacovalent phosphorus of the transition state, relative to other catalytic residues. If compared to the corresponding wild-type data, the structural implications of the mutation in the present crystal structure of Phe 100 Ala RNase T1 complexed with the specific inhibitor 2'-GMP are restricted to the active site. Repositioning of 2'-GMP, caused by the Phe 100 Ala mutation, generates new or improved contacts of the phosphate moiety with Arg 77 and His 92. In contrast, interactions with the Glu 58 carboxylate appear to be weakened. The effects of the His 92 Gln and Phe 100 Ala mutations on GpC turnover are additive in the corresponding double mutant, indicating that the contribution of Phe 100 to catalysis is independent of the catalytic acid His 92. The present results lead to the conclusion that apolar residues may contribute considerably to catalyze conversions of charged molecules to charged products, involving even more polar transition states.

About this Structure

1BIR is a Single protein structure of sequence from Aspergillus oryzae. Full crystallographic information is available from OCA.

Reference

A catalytic function for the structurally conserved residue Phe 100 of ribonuclease T1., Doumen J, Gonciarz M, Zegers I, Loris R, Wyns L, Steyaert J, Protein Sci. 1996 Aug;5(8):1523-30. PMID:8844843

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