1swt
From Proteopedia
(New page: 200px<br /><applet load="1swt" size="450" color="white" frame="true" align="right" spinBox="true" caption="1swt, resolution 2.00Å" /> '''CORE-STREPTAVIDIN MU...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1swt.gif|left|200px]]<br /><applet load="1swt" size=" | + | [[Image:1swt.gif|left|200px]]<br /><applet load="1swt" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1swt, resolution 2.00Å" /> | caption="1swt, resolution 2.00Å" /> | ||
'''CORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5'''<br /> | '''CORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5'''<br /> | ||
==Overview== | ==Overview== | ||
| - | It is currently unclear whether small molecules dissociate from a protein | + | It is currently unclear whether small molecules dissociate from a protein binding site along a defined pathway or through a collection of dissociation pathways. We report herein a joint crystallographic, computational, and biophysical study that suggests the Asp-128 --> Ala (D128A) streptavidin mutant closely mimics an intermediate on a well-defined dissociation pathway. Asp-128 is hydrogen bonded to a ureido nitrogen of biotin and also networks with the important aromatic binding contacts Trp-92 and Trp-108. The Asn-23 hydrogen bond to the ureido oxygen of biotin is lengthened to 3.8 A in the D128A structure, and a water molecule has moved into the pocket to replace the missing carboxylate interaction. These alterations are accompanied by the coupled movement of biotin, the flexible binding loop containing Ser-45, and the loop containing the Ser-27 hydrogen bonding contact. This structure closely parallels a key intermediate observed in a potential of mean force-simulated dissociation pathway of native streptavidin, where the Asn-23 hydrogen bond breaks first, accompanied by the replacement of the Asp-128 hydrogen bond by an entering water molecule. Furthermore, both biotin and the flexible loop move in a concerted conformational change that closely approximates the D128A structural changes. The activation and thermodynamic parameters for the D128A mutant were measured and are consistent with an intermediate that has traversed the early portion of the dissociation reaction coordinate through endothermic bond breaking and concomitant gain in configurational entropy. These composite results suggest that the D128A mutant provides a structural "snapshot" of an early intermediate on a relatively well-defined dissociation pathway for biotin. |
==About this Structure== | ==About this Structure== | ||
| - | 1SWT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii] with BTN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1SWT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii] with <scene name='pdbligand=BTN:'>BTN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWT OCA]. |
==Reference== | ==Reference== | ||
| Line 15: | Line 15: | ||
[[Category: Chu, V.]] | [[Category: Chu, V.]] | ||
[[Category: Freitag, S.]] | [[Category: Freitag, S.]] | ||
| - | [[Category: Klumb, L | + | [[Category: Klumb, L A.]] |
| - | [[Category: Stayton, P | + | [[Category: Stayton, P S.]] |
| - | [[Category: Stenkamp, R | + | [[Category: Stenkamp, R E.]] |
| - | [[Category: Trong, I | + | [[Category: Trong, I Le.]] |
[[Category: BTN]] | [[Category: BTN]] | ||
[[Category: biotin binding protein]] | [[Category: biotin binding protein]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:06:08 2008'' |
Revision as of 13:06, 21 February 2008
|
CORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5
Overview
It is currently unclear whether small molecules dissociate from a protein binding site along a defined pathway or through a collection of dissociation pathways. We report herein a joint crystallographic, computational, and biophysical study that suggests the Asp-128 --> Ala (D128A) streptavidin mutant closely mimics an intermediate on a well-defined dissociation pathway. Asp-128 is hydrogen bonded to a ureido nitrogen of biotin and also networks with the important aromatic binding contacts Trp-92 and Trp-108. The Asn-23 hydrogen bond to the ureido oxygen of biotin is lengthened to 3.8 A in the D128A structure, and a water molecule has moved into the pocket to replace the missing carboxylate interaction. These alterations are accompanied by the coupled movement of biotin, the flexible binding loop containing Ser-45, and the loop containing the Ser-27 hydrogen bonding contact. This structure closely parallels a key intermediate observed in a potential of mean force-simulated dissociation pathway of native streptavidin, where the Asn-23 hydrogen bond breaks first, accompanied by the replacement of the Asp-128 hydrogen bond by an entering water molecule. Furthermore, both biotin and the flexible loop move in a concerted conformational change that closely approximates the D128A structural changes. The activation and thermodynamic parameters for the D128A mutant were measured and are consistent with an intermediate that has traversed the early portion of the dissociation reaction coordinate through endothermic bond breaking and concomitant gain in configurational entropy. These composite results suggest that the D128A mutant provides a structural "snapshot" of an early intermediate on a relatively well-defined dissociation pathway for biotin.
About this Structure
1SWT is a Single protein structure of sequence from Streptomyces avidinii with as ligand. Full crystallographic information is available from OCA.
Reference
A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway., Freitag S, Chu V, Penzotti JE, Klumb LA, To R, Hyre D, Le Trong I, Lybrand TP, Stenkamp RE, Stayton PS, Proc Natl Acad Sci U S A. 1999 Jul 20;96(15):8384-9. PMID:10411884
Page seeded by OCA on Thu Feb 21 15:06:08 2008
