1kf5

From Proteopedia

(Difference between revisions)

Current revision

Atomic Resolution Structure of RNase A at pH 7.1

Structural highlights

1kf5 is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.15Å
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

The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.

Atomic resolution structures of ribonuclease A at six pH values.,Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):441-50. Epub 2002, Feb 21. PMID:11856829^[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
↑ Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L. Atomic resolution structures of ribonuclease A at six pH values. Acta Crystallogr D Biol Crystallogr. 2002 Mar;58(Pt 3):441-50. Epub 2002, Feb 21. PMID:11856829

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/1kf5"

@@ Line 1: / Line 1: @@
 ==Atomic Resolution Structure of RNase A at pH 7.1==
-<StructureSection load='1kf5' size='340' side='right' caption='[[1kf5]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
+<StructureSection load='1kf5' size='340' side='right'caption='[[1kf5]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1kf5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KF5 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kf2|1kf2]], [[1kf3|1kf3]], [[1kf4|1kf4]], [[1kf7|1kf7]], [[1kf8|1kf8]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</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'>[https://proteopedia.org/fgij/fg.htm?mol=1kf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kf5 OCA], [https://pdbe.org/1kf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kf5 RCSB], [https://www.ebi.ac.uk/pdbsum/1kf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kf5 ProSAT]</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=1kf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kf5 OCA], [http://pdbe.org/1kf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kf5 RCSB], [http://www.ebi.ac.uk/pdbsum/1kf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kf5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN]] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/1kf5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 31: / Line 30: @@
 ==See Also==
-*[[Temp|Temp]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 36: @@
 </StructureSection>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Berisio, R]]
+[[Category: Berisio R]]
-[[Category: Lamzin, V S]]
+[[Category: Lamzin VS]]
-[[Category: Mazzarella, L]]
+[[Category: Mazzarella L]]
-[[Category: Sica, F]]
+[[Category: Sica F]]
-[[Category: Wilson, K S]]
+[[Category: Wilson KS]]
-[[Category: Zagari, A]]
+[[Category: Zagari A]]
-[[Category: Crystal]]
-[[Category: Hydrolase]]
-[[Category: Ph]]
-[[Category: Rnase some]]
-[[Category: Soaking]]
-[[Category: Titration]]

1kf5

From Proteopedia

Current revision

Atomic Resolution Structure of RNase A at pH 7.1

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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