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2rdf

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Revision as of 11:45, 5 August 2016

Crystal Structure of staphyloccocal nuclease VIAGAN/E75A variant at cryogenic temperature

Structural highlights

2rdf 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.
Ligands:
Gene:	nuc (Staphylococcus aureus)
Activity:	Micrococcal nuclease, with EC number 3.1.31.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.

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

His121 and His124 are embedded in a network of polar and ionizable groups on the surface of staphylococcal nuclease. To examine how membership in a network affects the electrostatic properties of ionizable groups, the tautomeric state and the pK(a) values of these histidines were measured with NMR spectroscopy in the wild-type nuclease and in 13 variants designed to disrupt the network. In the background protein, His121 and His124 titrate with pK(a) values of 5.2 and 5.6, respectively. In the variants, where the network was disrupted, the pK(a) values range from 4.03 to 6.46 for His121, and 5.04 to 5.99 for His124. The largest decrease in a pK(a) was observed when the favorable Coulomb interaction between His121 and Glu75 was eliminated; the largest increase was observed when Tyr91 or Tyr93 was substituted with Ala or Phe. In all variants, the dominant tautomeric state at neutral pH was the N(epsilon2) state. At one level the network behaves as a rigid unit that does not readily reorganize when disrupted: crystal structures of the E75A or E75Q variants show that even when the pivotal Glu75 is removed, the overall configuration of the network was unaffected. On the other hand, a few key hydrogen bonds appear to govern the conformation of the network, and when these bonds are disrupted the network reorganizes. Coulomb interactions within the network report an effective dielectric constant of 20, whereas a dielectric constant of 80 is more consistent with the magnitude of medium to long-range Coulomb interactions in this protein. The data demonstrate that when structures are treated as static, rigid bodies, structure-based pK(a) calculations with continuum electrostatics method are not useful to treat ionizable groups in cases where pK(a) values are governed by short-range polar and Coulomb interactions.

Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease.,Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE J Mol Biol. 2008 Jun 20;379(5):1045-62. Epub 2008 Apr 16. PMID:18499123^[1]

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

References

↑ Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE. Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease. J Mol Biol. 2008 Jun 20;379(5):1045-62. Epub 2008 Apr 16. PMID:18499123 doi:10.1016/j.jmb.2008.04.021

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/2rdf"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of staphyloccocal nuclease VIAGAN/E75A variant at cryogenic temperature==
 <StructureSection load='2rdf' size='340' side='right' caption='[[2rdf]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <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='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='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=2rdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdf RCSB], [http://www.ebi.ac.uk/pdbsum/2rdf 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=2rdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdf OCA], [http://pdbe.org/2rdf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdf RCSB], [http://www.ebi.ac.uk/pdbsum/2rdf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdf ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2rdf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2rdf" style="background-color:#fffaf0;"></div>
 ==See Also==

2rdf

From Proteopedia

Revision as of 11:45, 5 August 2016

Crystal Structure of staphyloccocal nuclease VIAGAN/E75A variant at cryogenic 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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