2g2u: Difference between revisions

Revision as of 18:27, 21 February 2008

Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex

OverviewOverview

Beta-lactamase inhibitor protein (BLIP) binds a variety of class A beta-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of beta-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8A SHV D104K.BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant beta-lactamase.BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1.BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the beta-lactamase.BLIP complexes and computationally assisted design of tight binding BLIP variants.

About this StructureAbout this Structure

2G2U is a Protein complex structure of sequences from Klebsiella pneumoniae and Streptomyces clavuligerus. Active as Beta-lactamase, with EC number 3.5.2.6 Full crystallographic information is available from OCA.

ReferenceReference

Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface., Reynolds KA, Thomson JM, Corbett KD, Bethel CR, Berger JM, Kirsch JF, Bonomo RA, Handel TM, J Biol Chem. 2006 Sep 8;281(36):26745-53. Epub 2006 Jun 29. PMID:16809340

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-[[Image:2g2u.gif|left|200px]]<br /><applet load="2g2u" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2g2u.gif|left|200px]]<br /><applet load="2g2u" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2g2u, resolution 1.60&Aring;" />
 '''Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex'''<br />
 ==Overview==
-Beta-lactamase inhibitor protein (BLIP) binds a variety of class A, beta-lactamases with affinities ranging from micromolar to picomolar., Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally, identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1., Determining the underlying source of this affinity difference is important, for understanding the molecular basis of beta-lactamase inhibition and, mechanisms of protein-protein interface specificity and affinity. Here we, present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP, binding affinity from micromolar to nanomolar. Comparison of the, SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that, the increased volume of Glu-104 stabilizes a key binding loop in the, interface. Solution of the 1.8A SHV D104K.BLIP crystal structure, identifies a novel conformation in which this binding loop is removed from, the interface. Using these structural data, we evaluated the ability of, EGAD, a program developed for computational protein design, to calculate, changes in the stability of mutant beta-lactamase.BLIP complexes. Changes, in binding affinity were calculated within an error of 1.6 kcal/mol of the, experimental values for 112 mutations at the TEM-1.BLIP interface and, within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP, interface. The reasonable success of EGAD in predicting changes in, interface stability is a promising step toward understanding the stability, of the beta-lactamase.BLIP complexes and computationally assisted design, of tight binding BLIP variants.
+Beta-lactamase inhibitor protein (BLIP) binds a variety of class A beta-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of beta-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8A SHV D104K.BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant beta-lactamase.BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1.BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the beta-lactamase.BLIP complexes and computationally assisted design of tight binding BLIP variants.
 ==About this Structure==
-G2U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] and [http://en.wikipedia.org/wiki/Streptomyces_clavuligerus Streptomyces clavuligerus]. Active as [http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2G2U OCA].
+G2U is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] and [http://en.wikipedia.org/wiki/Streptomyces_clavuligerus Streptomyces clavuligerus]. Active as [http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G2U OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Protein complex]]
 [[Category: Streptomyces clavuligerus]]
-[[Category: Berger, J.M.]]
+[[Category: Berger, J M.]]
-[[Category: Bethel, C.R.]]
+[[Category: Bethel, C R.]]
-[[Category: Bonomo, R.A.]]
+[[Category: Bonomo, R A.]]
-[[Category: Corbett, K.D.]]
+[[Category: Corbett, K D.]]
-[[Category: Handel, T.M.]]
+[[Category: Handel, T M.]]
-[[Category: Kirsch, J.F.]]
+[[Category: Kirsch, J F.]]
-[[Category: Reynolds, K.A.]]
+[[Category: Reynolds, K A.]]
-[[Category: Thomson, J.M.]]
+[[Category: Thomson, J M.]]
 [[Category: beta-lactamase]]
 [[Category: beta-lactamase inhibitor]]
@@ Line 29: / Line 29: @@
 [[Category: shv-1]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:55:12 2007''
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