2gkr

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(Difference between revisions)

Revision as of 07:08, 20 June 2018

Crystal structure of the N-terminally truncated OMTKY3-del(1-5)

Structural highlights

2gkr is a 1 chain structure with sequence from Melga. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Sequence-to-reactivity algorithms (SRAs) for proteins have the potential of being broadly applied in molecular design. Recently, Laskowski et al. have reported an additivity-based SRA that accurately predicts most of the standard free energy changes of association for variants of turkey ovomucoid third domain (OMTKY3) with six serine peptidases, one of which is streptogrisin B (commonly known as Streptomyces griseus peptidase B, SGPB). Non-additivity effects for residues 18I and 32I, and for residues 20I and 32I of OMTKY3 occurred when the associations with SGPB were predicted using the SRA. To elucidate precisely the mechanics of these non-additivity effects in structural terms, we have determined the crystal structures of the unbound OMTKY3 (with Gly32I as in the wild-type amino acid sequence) at a resolution of 1.16 A, the unbound Ala32I variant of OMTKY3 at a resolution of 1.23 A, and the SGPB:OMTKY3-Ala32I complex (equilibrium association constant K(a)=7.1x10(9) M(-1) at 21(+/-2) C degrees, pH 8.3) at a resolution of 1.70 A. Extensive comparisons with the crystal structure of the unbound OMTKY3 confirm our understanding of some previously addressed non-additivity effects. Unexpectedly, SGPB and OMTKY3-Ala32I form a 1:2 complex in the crystal. Comparison with the SGPB:OMTKY3 complex shows a conformational change in the SGPB:OMTKY3-Ala32I complex, resulting from a hinged rigid-body rotation of the inhibitor caused by the steric hindrance between the methyl group of Ala32IA of the inhibitor and Pro192BE of the peptidase. This perturbs the interactions among residues 18I, 20I, 32I and 36I of the inhibitor, probably resulting in the above non-additivity effects. This conformational change also introduces residue 10I as an additional hyper-variable contact residue to the SRA.

Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors.,Lee TW, Qasim MA, Laskowski M Jr, James MN J Mol Biol. 2007 Mar 23;367(2):527-46. Epub 2007 Jan 9. PMID:17266986^[1]

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

References

↑ Lee TW, Qasim MA, Laskowski M Jr, James MN. Structural insights into the non-additivity effects in the sequence-to-reactivity algorithm for serine peptidases and their inhibitors. J Mol Biol. 2007 Mar 23;367(2):527-46. Epub 2007 Jan 9. PMID:17266986 doi:10.1016/j.jmb.2007.01.008

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2gkr"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the N-terminally truncated OMTKY3-del(1-5)==
 <StructureSection load='2gkr' size='340' side='right' caption='[[2gkr]], [[Resolution|resolution]] 1.16&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gkr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_turkey Common turkey]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GKR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gkr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Melga Melga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GKR FirstGlance]. <br>
 </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='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=2gkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gkr OCA], [http://pdbe.org/2gkr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gkr RCSB], [http://www.ebi.ac.uk/pdbsum/2gkr 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=2gkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gkr OCA], [http://pdbe.org/2gkr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gkr RCSB], [http://www.ebi.ac.uk/pdbsum/2gkr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gkr ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 10: / Line 11: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gk/2gkr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gk/2gkr_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/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=2gkr ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 30: @@
 __TOC__
 </StructureSection>
-[[Category: Common turkey]]
+[[Category: Melga]]
 [[Category: James, M N.G]]
 [[Category: Laskowski, M]]

2gkr

From Proteopedia

Revision as of 07:08, 20 June 2018

Crystal structure of the N-terminally truncated OMTKY3-del(1-5)

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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