1w4p
From Proteopedia
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|PDB= 1w4p |SIZE=350|CAPTION= <scene name='initialview01'>1w4p</scene>, resolution 1.69Å | |PDB= 1w4p |SIZE=350|CAPTION= <scene name='initialview01'>1w4p</scene>, resolution 1.69Å | ||
|SITE= <scene name='pdbsite=AC1:Um3+Binding+Site+For+Chain+B'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Um3+Binding+Site+For+Chain+B'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=UM3:2'-DEOXYURIDINE 3'-MONOPHOSPHATE'>UM3</scene> | + | |LIGAND= <scene name='pdbligand=UM3:2'-DEOXYURIDINE+3'-MONOPHOSPHATE'>UM3</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1w4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w4p OCA], [http://www.ebi.ac.uk/pdbsum/1w4p PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1w4p RCSB]</span> | ||
}} | }} | ||
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[[Category: Sweeney, R Y.]] | [[Category: Sweeney, R Y.]] | ||
[[Category: Thiyagarajan, N.]] | [[Category: Thiyagarajan, N.]] | ||
| - | [[Category: UM3]] | ||
[[Category: endonuclease]] | [[Category: endonuclease]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
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[[Category: rnase some]] | [[Category: rnase some]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:31:07 2008'' |
Revision as of 21:31, 30 March 2008
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| , resolution 1.69Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | |||||||
| Activity: | Pancreatic ribonuclease, with EC number 3.1.27.5 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
BINDING OF NONNATURAL 3'-NUCLEOTIDES TO RIBONUCLEASE A
Overview
2'-Fluoro-2'-deoxyuridine 3'-phosphate (dU(F)MP) and arabinouridine 3'-phosphate (araUMP) have non-natural furanose rings. dU(F)MP and araUMP were prepared by chemical synthesis and found to have three- to sevenfold higher affinity than uridine 3'-phosphate (3'-UMP) or 2'-deoxyuridine 3'-phosphate (dUMP) for ribonuclease A (RNase A). These differences probably arise (in part) from the phosphoryl groups of 3'-UMP, dU(F)MP, and araUMP (pK(a) = 5.9) being more anionic than that of dUMP (pK(a) = 6.3). The three-dimensional structures of the crystalline complexes of RNase A with dUMP, dU(F)MP and araUMP were determined at < 1.7 A resolution by X-ray diffraction analysis. In these three structures, the uracil nucleobases and phosphoryl groups bind to the enzyme in a nearly identical position. Unlike 3'-UMP and dU(F)MP, dUMP and araUMP bind with their furanose rings in the preferred pucker. In the RNase A.araUMP complex, the 2'-hydroxyl group is exposed to the solvent. All four 3'-nucleotides bind more tightly to wild-type RNase A than to its T45G variant, which lacks the residue that interacts most closely with the uracil nucleobase. These findings illuminate in atomic detail the interaction of RNase A and 3'-nucleotides, and indicate that non-natural furanose rings can serve as the basis for more potent inhibitors of catalysis by RNase A.
About this Structure
1W4P is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
Binding of non-natural 3'-nucleotides to ribonuclease A., Jenkins CL, Thiyagarajan N, Sweeney RY, Guy MP, Kelemen BR, Acharya KR, Raines RT, FEBS J. 2005 Feb;272(3):744-55. PMID:15670155
Page seeded by OCA on Mon Mar 31 00:31:07 2008
