2pqe

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:44, 22 May 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2pqe.gif|left|200px]]
 
-
{{Structure
+
==Solution structure of proline-free mutant of staphylococcal nuclease==
-
|PDB= 2pqe |SIZE=350|CAPTION= <scene name='initialview01'>2pqe</scene>
+
<StructureSection load='2pqe' size='340' side='right'caption='[[2pqe]]' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND=
+
<table><tr><td colspan='2'>[[2pqe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PQE FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
|GENE= nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pqe OCA], [https://pdbe.org/2pqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pqe RCSB], [https://www.ebi.ac.uk/pdbsum/2pqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pqe ProSAT]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pqe OCA], [http://www.ebi.ac.uk/pdbsum/2pqe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pqe RCSB]</span>
+
[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
-
}}
+
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pq/2pqe_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pqe ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The role of cis-trans isomerizations of peptidyl-proline bonds in the enzyme activity of staphylococcal nuclease (SNase) was examined by mutation of proline residues. The proline-free SNase ([Pro-]SNase), namely, P11A/P31A/P42A/P47T/P56A/P117G-mutant SNase, was adopted for elucidating the correlation between the nuclease activity and the backbone conformational and dynamic states of SNase. The 3D solution structure of [Pro-]SNase has been determined by heteronuclear NMR experiments. Comparing the structure of [Pro-]SNase with the structure of SNase revealed the conformational differences between the two proteins. In the structure of [Pro-]SNase, conformational rearrangements were observed for the loop of residues Ala112-His121 containing a trans Lys116-Gly117 peptide bond and for the C-terminal alpha-helical loop of residues Leu137-Glu142. Mutation of proline at position 117 also caused the conformational rearrangement of the p-loop (Asp77-Leu89), which is remote from the Ala112-His121 loop. The Ala112-His121 loop and p-loop are placed closer to each other in [Pro-]SNase than in SNase. The backbone dynamic features of the omega-loop (Pro42-Pro56) of SNase are different from those of [Pro-]SNase. The backbone of the omega-loop exhibits restricted flexibility with slow conformational exchange motions in SNase, but is highly flexible in [Pro-]SNase. The analysis indicates that the restrained backbone conformation of the Ala112-His121 loop and restricted flexibility of the omega-loop are two dominant factors determining the enzyme activity of SNase. Of the two factors, the former is correlated with the strained cis Lys116-Pro117 peptide bond and the latter is correlated with the cis-trans isomerizations of the His46-Pro47 peptide bond.
-
'''Solution structure of proline-free mutant of staphylococcal nuclease'''
+
Restricted backbone conformational and motional flexibilities of loops containing peptidyl-proline bonds dominate the enzyme activity of staphylococcal nuclease.,Shan L, Tong Y, Xie T, Wang M, Wang J Biochemistry. 2007 Oct 16;46(41):11504-13. Epub 2007 Sep 22. PMID:17887731<ref>PMID:17887731</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2pqe" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
The role of cis-trans isomerizations of peptidyl-proline bonds in the enzyme activity of staphylococcal nuclease (SNase) was examined by mutation of proline residues. The proline-free SNase ([Pro-]SNase), namely, P11A/P31A/P42A/P47T/P56A/P117G-mutant SNase, was adopted for elucidating the correlation between the nuclease activity and the backbone conformational and dynamic states of SNase. The 3D solution structure of [Pro-]SNase has been determined by heteronuclear NMR experiments. Comparing the structure of [Pro-]SNase with the structure of SNase revealed the conformational differences between the two proteins. In the structure of [Pro-]SNase, conformational rearrangements were observed for the loop of residues Ala112-His121 containing a trans Lys116-Gly117 peptide bond and for the C-terminal alpha-helical loop of residues Leu137-Glu142. Mutation of proline at position 117 also caused the conformational rearrangement of the p-loop (Asp77-Leu89), which is remote from the Ala112-His121 loop. The Ala112-His121 loop and p-loop are placed closer to each other in [Pro-]SNase than in SNase. The backbone dynamic features of the omega-loop (Pro42-Pro56) of SNase are different from those of [Pro-]SNase. The backbone of the omega-loop exhibits restricted flexibility with slow conformational exchange motions in SNase, but is highly flexible in [Pro-]SNase. The analysis indicates that the restrained backbone conformation of the Ala112-His121 loop and restricted flexibility of the omega-loop are two dominant factors determining the enzyme activity of SNase. Of the two factors, the former is correlated with the strained cis Lys116-Pro117 peptide bond and the latter is correlated with the cis-trans isomerizations of the His46-Pro47 peptide bond.
+
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
2PQE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PQE OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Large Structures]]
-
Restricted backbone conformational and motional flexibilities of loops containing peptidyl-proline bonds dominate the enzyme activity of staphylococcal nuclease., Shan L, Tong Y, Xie T, Wang M, Wang J, Biochemistry. 2007 Oct 16;46(41):11504-13. Epub 2007 Sep 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17887731 17887731]
+
-
[[Category: Micrococcal nuclease]]
+
-
[[Category: Single protein]]
+
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
-
[[Category: Shan, L.]]
+
[[Category: Shan L]]
-
[[Category: Tong, Y.]]
+
[[Category: Tong Y]]
-
[[Category: Wang, J.]]
+
[[Category: Wang J]]
-
[[Category: Wang, M.]]
+
[[Category: Wang M]]
-
[[Category: Xie, T.]]
+
[[Category: Xie T]]
-
[[Category: beta barrel]]
+
-
[[Category: hydrolase]]
+
-
[[Category: ob fold]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:39:20 2008''
+

Current revision

Solution structure of proline-free mutant of staphylococcal nuclease

PDB ID 2pqe

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pqe"
Personal tools