This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1zsz

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:22, 2 May 2018

Crystal structure of a computationally designed SspB heterodimer

Structural highlights

1zsz is a 3 chain structure with sequence from "bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	sspB ("Bacterium influenzae" Lehmann and Neumann 1896)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SSPB_HAEIN] Enhances recognition of ssrA-tagged proteins by the ClpX-ClpP protease; the ssrA degradation tag (AANDENYALAA) is added trans-translationally to proteins that are stalled on the ribosome, freeing the ribosome and targeting stalled peptides for degradation. SspB activates the ATPase activity of ClpX. Seems to act in concert with SspA in the regulation of several proteins during exponential and stationary-phase growth (By similarity). Also stimulates degradation of the N-terminus of RseA (residues 1-108, alone or in complex with sigma-E) by ClpX-ClpP in a non-ssrA-mediated fashion (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

Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and/or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more stable than the specificity-design heterodimer (positive and negative design). By contrast, only the specificity-design protein assembled as a homogenous heterodimer in solution, whereas the stability-design protein formed a mixture of homodimer and heterodimer species. The experimental stabilities of the engineered proteins correlated roughly with their calculated stabilities, and the crystal structure of the specificity-design heterodimer showed most of the predicted side-chain packing interactions and a main-chain conformation indistinguishable from the wild-type structure. These results indicate that the design simulations capture important features of both stability and structure and demonstrate that negative design can be critical for attaining specificity when competing states are close in structure space.

Specificity versus stability in computational protein design.,Bolon DN, Grant RA, Baker TA, Sauer RT Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12724-9. Epub 2005 Aug 29. PMID:16129838^[1]

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

References

↑ Bolon DN, Grant RA, Baker TA, Sauer RT. Specificity versus stability in computational protein design. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12724-9. Epub 2005 Aug 29. PMID:16129838

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of a computationally designed SspB heterodimer==
 <StructureSection load='1zsz' size='340' side='right' caption='[[1zsz]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=1zsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zsz OCA], [http://pdbe.org/1zsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zsz RCSB], [http://www.ebi.ac.uk/pdbsum/1zsz 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=1zsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zsz OCA], [http://pdbe.org/1zsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zsz RCSB], [http://www.ebi.ac.uk/pdbsum/1zsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zsz ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zs/1zsz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zs/1zsz_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1zsz

From Proteopedia

Revision as of 09:22, 2 May 2018

Crystal structure of a computationally designed SspB heterodimer

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox