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.

2za4

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 01:35, 9 February 2016

Crystal Structural Analysis of Barnase-barstar Complex

Structural highlights

2za4 is a 4 chain structure with sequence from Bacillus amyloliquefaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1x1u, 1x1w, 1x1x, 1x1y
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[RNBR_BACAM] Hydrolyzes phosphodiester bonds in RNA, poly- and oligoribonucleotides resulting in 3'-nucleoside monophosphates via 2',3'-cyclophosphate intermediates. [BARS_BACAM] Inhibitor of the ribonuclease barnase. Forms a one-to-one non-covalent complex.

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 complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein-protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 --> Ala, which corresponds to a change of 7.7 kcal x mol(-1) in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 A resolution by X-ray crystallography. The complex was similar to the wild-type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel-like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel-like structure of hydrated water molecules.

Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation.,Urakubo Y, Ikura T, Ito N Protein Sci. 2008 Jun;17(6):1055-65. Epub 2008 Apr 25. PMID:18441234^[1]

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

References

↑ Urakubo Y, Ikura T, Ito N. Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation. Protein Sci. 2008 Jun;17(6):1055-65. Epub 2008 Apr 25. PMID:18441234 doi:10.1110/ps.073322508

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/2za4"

@@ Line 5: / Line 5: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x1u|1x1u]], [[1x1w|1x1w]], [[1x1x|1x1x]], [[1x1y|1x1y]]</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=2za4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2za4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2za4 RCSB], [http://www.ebi.ac.uk/pdbsum/2za4 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=2za4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2za4 OCA], [http://pdbe.org/2za4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2za4 RCSB], [http://www.ebi.ac.uk/pdbsum/2za4 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
     <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=2za4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2za4" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 33: / Line 34: @@
 *[[Ribonuclease|Ribonuclease]]
 *[[Temp|Temp]]
-*[[User:Jaime.Prilusky/Test/tree|User:Jaime.Prilusky/Test/tree]]
 == References ==
 <references/>

2za4

From Proteopedia

Revision as of 01:35, 9 February 2016

Crystal Structural Analysis of Barnase-barstar Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox