2vek: Difference between revisions

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Revision as of 19:45, 20 March 2008

File:2vek.jpg

, resolution 1.60Å

Sites:

, , and

Ligands:

, and

Activity:

Triose-phosphate isomerase, with EC number 5.3.1.1

Coordinates:

save as pdb, mmCIF, xml

STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES

OverviewOverview

A monomeric variant of triosephosphate isomerase (TIM) with a new engineered binding groove has been characterized further. In this variant (ml8bTIM), the phosphate binding loop had been shortened, causing the binding site to be much more extended. Here, it is reported that in the V233A variant of ml8bTIM (A-TIM), three important properties of the wild-type TIM active site have been restored: (i) the structural properties of loop-7, (ii) the binding site of a conserved water molecule between loop-7 and loop-8 and (iii) the binding site of the phosphate moiety. It is shown that the active site of A-TIM can bind TIM transition state analogs and suicide inhibitors competently. It is found that the active site geometry of the A-TIM complexes is less compact and more solvent exposed, as in wild-type TIM. This correlates with the observation that the catalytic efficiency of A-TIM for interconverting the TIM substrates is too low to be detected. It is also shown that the A-TIM active site can bind compounds which do not bind to wild-type TIM and which are completely different from the normal TIM substrate, like a citrate molecule. The binding of this citrate molecule is stabilized by hydrogen bonding interactions with the new binding groove.

About this StructureAbout this Structure

2VEK is a Single protein structure of sequence from Trypanosoma brucei brucei. Full crystallographic information is available from OCA.

ReferenceReference

Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties., Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P, Wierenga RK, Protein Eng Des Sel. 2008 Jan 31;. PMID:18239072

Page seeded by OCA on Thu Mar 20 18:45:43 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2vek.jpg|left|200px]]<br /><applet load="2vek" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2vek.jpg|left|200px]]
-caption="2vek, resolution 1.60&Aring;" />
-'''STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES'''<br />
+ {{Structure
+|PDB= 2vek |SIZE=350|CAPTION= <scene name='initialview01'>2vek</scene>, resolution 1.60&Aring;
+|SITE= <scene name='pdbsite=AC1:Cit+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cit+Binding+Site+For+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Tbu+Binding+Site+For+Chain+B'>AC3</scene> and <scene name='pdbsite=AC4:A74+Binding+Site+For+Chain+B'>AC4</scene>
+|LIGAND= <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ASF:'>ASF</scene> and <scene name='pdbligand=TBU:TERTIARY-BUTYL ALCOHOL'>TBU</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1]
+|GENE=
+}}
+'''STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-VEK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei] with <scene name='pdbligand=CIT:'>CIT</scene>, <scene name='pdbligand=ASF:'>ASF</scene> and <scene name='pdbligand=TBU:'>TBU</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] Known structural/functional Sites: <scene name='pdbsite=AC1:Cit+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cit+Binding+Site+For+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Tbu+Binding+Site+For+Chain+B'>AC3</scene> and <scene name='pdbsite=AC4:A74+Binding+Site+For+Chain+B'>AC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEK OCA].
+VEK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEK OCA].
 ==Reference==
-Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties., Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P, Wierenga RK, Protein Eng Des Sel. 2008 Jan 31;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18239072 18239072]
+Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties., Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P, Wierenga RK, Protein Eng Des Sel. 2008 Jan 31;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18239072 18239072]
 [[Category: Single protein]]
 [[Category: Triose-phosphate isomerase]]
@@ Line 41: / Line 50: @@
 [[Category: triosephosphate isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:55:19 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:45:43 2008''