1w4p

From Proteopedia

(Difference between revisions)

Revision as of 07:18, 4 April 2018

Binding of Nonnatural 3'-Nucleotides to Ribonuclease A

Structural highlights

1w4p is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1a2w, 1a5p, 1a5q, 1afk, 1afl, 1afu, 1aqp, 1b6v, 1bel, 1bzq, 1c0b, 1c0c, 1c8w, 1c9v, 1c9x, 1cjq, 1cjr, 1d5d, 1d5e, 1d5h, 1dfj, 1dy5, 1eic, 1eid, 1eie, 1eos, 1eow, 1f0v, 1fev, 1fs3, 1gv7, 1izp, 1izq, 1izr, 1j7z, 1j80, 1j81, 1j82, 1jn4, 1js0, 1jvt, 1jvu, 1jvv, 1kf2, 1kf3, 1kf4, 1kf5, 1kf7, 1kf8, 1kh8, 1lsq, 1o0f, 1o0h, 1o0m, 1o0n, 1o0o, 1qhc, 1rar, 1ras, 1rat, 1rbb, 1rbc, 1rbd, 1rbe, 1rbf, 1rbg, 1rbh, 1rbi, 1rbj, 1rbn, 1rbw, 1rbx, 1rca, 1rcn, 1rha, 1rhb, 1rnc, 1rnd, 1rnm, 1rnn, 1rno, 1rnq, 1rnu, 1rnv, 1rnw, 1rnx, 1rny, 1rnz, 1rob, 1rpf, 1rpg, 1rph, 1rsm, 1rta, 1rtb, 1ruv, 1srn, 1ssa, 1ssb, 1ssc, 1un5, 1w4o, 1w4q, 1xps, 1xpt, 2aas, 2rat, 2rln, 2rns, 3rat, 3rn3, 3rsd, 3rsk, 3rsp, 3srn, 4rat, 4rsd, 4rsk, 4srn, 5rat, 5rsa, 6rat, 6rsa, 7rat, 7rsa, 8rat, 8rsa, 9rat, 9rsa
Activity:	Pancreatic ribonuclease, with EC number 3.1.27.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
↑ Jenkins CL, Thiyagarajan N, Sweeney RY, Guy MP, Kelemen BR, Acharya KR, Raines RT. Binding of non-natural 3'-nucleotides to ribonuclease A. FEBS J. 2005 Feb;272(3):744-55. PMID:15670155 doi:http://dx.doi.org/10.1111/j.1742-4658.2004.04511.x

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1w4p"

@@ Line 1: / Line 1: @@
-==BINDING OF NONNATURAL 3'-NUCLEOTIDES TO RIBONUCLEASE A==
+==Binding of Nonnatural 3'-Nucleotides to Ribonuclease A==
 <StructureSection load='1w4p' size='340' side='right' caption='[[1w4p]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
 == Structural highlights ==
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a2w|1a2w]], [[1a5p|1a5p]], [[1a5q|1a5q]], [[1afk|1afk]], [[1afl|1afl]], [[1afu|1afu]], [[1aqp|1aqp]], [[1b6v|1b6v]], [[1bel|1bel]], [[1bzq|1bzq]], [[1c0b|1c0b]], [[1c0c|1c0c]], [[1c8w|1c8w]], [[1c9v|1c9v]], [[1c9x|1c9x]], [[1cjq|1cjq]], [[1cjr|1cjr]], [[1d5d|1d5d]], [[1d5e|1d5e]], [[1d5h|1d5h]], [[1dfj|1dfj]], [[1dy5|1dy5]], [[1eic|1eic]], [[1eid|1eid]], [[1eie|1eie]], [[1eos|1eos]], [[1eow|1eow]], [[1f0v|1f0v]], [[1fev|1fev]], [[1fs3|1fs3]], [[1gv7|1gv7]], [[1izp|1izp]], [[1izq|1izq]], [[1izr|1izr]], [[1j7z|1j7z]], [[1j80|1j80]], [[1j81|1j81]], [[1j82|1j82]], [[1jn4|1jn4]], [[1js0|1js0]], [[1jvt|1jvt]], [[1jvu|1jvu]], [[1jvv|1jvv]], [[1kf2|1kf2]], [[1kf3|1kf3]], [[1kf4|1kf4]], [[1kf5|1kf5]], [[1kf7|1kf7]], [[1kf8|1kf8]], [[1kh8|1kh8]], [[1lsq|1lsq]], [[1o0f|1o0f]], [[1o0h|1o0h]], [[1o0m|1o0m]], [[1o0n|1o0n]], [[1o0o|1o0o]], [[1qhc|1qhc]], [[1rar|1rar]], [[1ras|1ras]], [[1rat|1rat]], [[1rbb|1rbb]], [[1rbc|1rbc]], [[1rbd|1rbd]], [[1rbe|1rbe]], [[1rbf|1rbf]], [[1rbg|1rbg]], [[1rbh|1rbh]], [[1rbi|1rbi]], [[1rbj|1rbj]], [[1rbn|1rbn]], [[1rbw|1rbw]], [[1rbx|1rbx]], [[1rca|1rca]], [[1rcn|1rcn]], [[1rha|1rha]], [[1rhb|1rhb]], [[1rnc|1rnc]], [[1rnd|1rnd]], [[1rnm|1rnm]], [[1rnn|1rnn]], [[1rno|1rno]], [[1rnq|1rnq]], [[1rnu|1rnu]], [[1rnv|1rnv]], [[1rnw|1rnw]], [[1rnx|1rnx]], [[1rny|1rny]], [[1rnz|1rnz]], [[1rob|1rob]], [[1rpf|1rpf]], [[1rpg|1rpg]], [[1rph|1rph]], [[1rsm|1rsm]], [[1rta|1rta]], [[1rtb|1rtb]], [[1ruv|1ruv]], [[1srn|1srn]], [[1ssa|1ssa]], [[1ssb|1ssb]], [[1ssc|1ssc]], [[1un5|1un5]], [[1w4o|1w4o]], [[1w4q|1w4q]], [[1xps|1xps]], [[1xpt|1xpt]], [[2aas|2aas]], [[2rat|2rat]], [[2rln|2rln]], [[2rns|2rns]], [[3rat|3rat]], [[3rn3|3rn3]], [[3rsd|3rsd]], [[3rsk|3rsk]], [[3rsp|3rsp]], [[3srn|3srn]], [[4rat|4rat]], [[4rsd|4rsd]], [[4rsk|4rsk]], [[4srn|4srn]], [[5rat|5rat]], [[5rsa|5rsa]], [[6rat|6rat]], [[6rsa|6rsa]], [[7rat|7rat]], [[7rsa|7rsa]], [[8rat|8rat]], [[8rsa|8rsa]], [[9rat|9rat]], [[9rsa|9rsa]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1w4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w4p RCSB], [http://www.ebi.ac.uk/pdbsum/1w4p PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1w4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w4p RCSB], [http://www.ebi.ac.uk/pdbsum/1w4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w4p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w4/1w4p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w4/1w4p_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1w4p

From Proteopedia

Revision as of 07:18, 4 April 2018

Binding of Nonnatural 3'-Nucleotides to Ribonuclease A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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