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2pyk

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Revision as of 15:36, 17 June 2021

Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature

Structural highlights

2pyk is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1u9r, 2pw5, 2pw7
Gene:	nuc (Staphylococcus aureus)
Activity:	Micrococcal nuclease, with EC number 3.1.31.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NUC_STAAW] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond (By similarity).

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

Although internal water molecules are essential for the structure and function of many proteins, the structural and physical factors that govern internal hydration are poorly understood. We have examined the molecular determinants of internal hydration systematically, by solving the crystal structures of variants of staphylococcal nuclease with Gln-66, Asn-66, and Tyr-66 at cryo (100 K) and room (298 K) temperatures, and comparing them with existing cryo and room temperature structures of variants with Glu-66, Asp-66, Lys-66, Glu-92 or Lys-92 obtained under conditions of pH where the internal ionizable groups are in the neutral state. At cryogenic temperatures the polar moieties of all these internal side chains are hydrated except in the cases of Lys-66 and Lys-92. At room temperature the internal water molecules were observed only in variants with Glu-66 and Tyr-66; water molecules in the other variants are probably present but they are disordered and therefore undetectable crystallographically. Each internal water molecule establishes between 3 and 5 hydrogen bonds with the protein or with other internal water molecules. The strength of interactions between internal polar side chains and water molecules seems to decrease from carboxylic acids to amides to amines. Low temperature, low cavity volume, and the presence of oxygen atoms in the cavity increase the positional stability of internal water molecules. This set of structures and the physical insight they contribute into internal hydration will be useful for the development and benchmarking of computational methods for artificial hydration of pockets, cavities, and active sites in proteins.

Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.,Schlessman JL, Abe C, Gittis A, Karp DA, Dolan MA, Garcia-Moreno E B Biophys J. 2008 Apr 15;94(8):3208-16. Epub 2008 Jan 4. PMID:18178652^[1]

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

References

↑ Schlessman JL, Abe C, Gittis A, Karp DA, Dolan MA, Garcia-Moreno E B. Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Biophys J. 2008 Apr 15;94(8):3208-16. Epub 2008 Jan 4. PMID:18178652 doi:http://dx.doi.org/10.1529/biophysj.107.122473

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/2pyk"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature==
-<StructureSection load='2pyk' size='340' side='right' caption='[[2pyk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2pyk' size='340' side='right'caption='[[2pyk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pyk]] is a 1 chain structure with 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=2PYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PYK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pyk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYK FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u9r|1u9r]], [[2pw5|2pw5]], [[2pw7|2pw7]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u9r|1u9r]], [[2pw5|2pw5]], [[2pw7|2pw7]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nuc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nuc ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </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=2pyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyk OCA], [http://pdbe.org/2pyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyk RCSB], [http://www.ebi.ac.uk/pdbsum/2pyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyk ProSAT]</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=2pyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyk OCA], [https://pdbe.org/2pyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyk RCSB], [https://www.ebi.ac.uk/pdbsum/2pyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NUC_STAAW NUC_STAAW]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond (By similarity).
+[[https://www.uniprot.org/uniprot/NUC_STAAW NUC_STAAW]] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Staphylococcal nuclease|Staphylococcal nuclease]]
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Micrococcal nuclease]]
 [[Category: Staphylococcus aureus]]

2pyk

From Proteopedia

Revision as of 15:36, 17 June 2021

Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature

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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