1n9b: Difference between revisions

Revision as of 15:03, 21 February 2008

Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme

OverviewOverview

Bacterial beta-lactamases hydrolyze beta-lactam antibiotics such as penicillins and cephalosporins. The TEM-type class A beta-lactamase SHV-2 is a natural variant that exhibits activity against third-generation cephalosporins normally resistant to hydrolysis by class A enzymes. SHV-2 contains a single Gly238Ser change relative to the wild-type enzyme SHV-1. Crystallographic refinement of a model including hydrogen atoms gave R and R(free) of 12.4% and 15.0% for data to 0.91 A resolution. The hydrogen atom on the O(gamma) atom of the reactive Ser70 is clearly seen for the first time, bridging to the water molecule activated by Glu166. Though hydrogen atoms on the nearby Lys73 are not seen, this observation of the Ser70 hydrogen atom and the hydrogen bonding pattern around Lys73 indicate that Lys73 is protonated. These findings support a role for the Glu166-water couple, rather than Lys73, as the general base in the deprotonation of Ser70 in the acylation process of class A beta-lactamases. Overlay of SHV-2 with SHV-1 shows a significant 1-3 A displacement in the 238-242 beta-strand-turn segment, making the beta-lactam binding site more open to newer cephalosporins with large C7 substituents and thereby expanding the substrate spectrum of the variant enzyme. The OH group of the buried Ser238 side-chain hydrogen bonds to the main-chain CO of Asn170 on the Omega loop, that is unaltered in position relative to SHV-1. This structural role for Ser238 in protein-protein binding makes less likely its hydrogen bonding to oximino cephalosporins such as cefotaxime or ceftazidime.

About this StructureAbout this Structure

1N9B is a Single protein structure of sequence from Klebsiella pneumoniae with , and as ligands. Active as Beta-lactamase, with EC number 3.5.2.6 Full crystallographic information is available from OCA.

ReferenceReference

Ultrahigh resolution structure of a class A beta-lactamase: on the mechanism and specificity of the extended-spectrum SHV-2 enzyme., Nukaga M, Mayama K, Hujer AM, Bonomo RA, Knox JR, J Mol Biol. 2003 Apr 18;328(1):289-301. PMID:12684014

Page seeded by OCA on Thu Feb 21 14:03:39 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1n9b.jpg|left|200px]]<br /><applet load="1n9b" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1n9b.jpg|left|200px]]<br /><applet load="1n9b" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1n9b, resolution 0.90&Aring;" />
 '''Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme'''<br />
 ==Overview==
-Bacterial beta-lactamases hydrolyze beta-lactam antibiotics such as, penicillins and cephalosporins. The TEM-type class A beta-lactamase SHV-2, is a natural variant that exhibits activity against third-generation, cephalosporins normally resistant to hydrolysis by class A enzymes. SHV-2, contains a single Gly238Ser change relative to the wild-type enzyme SHV-1., Crystallographic refinement of a model including hydrogen atoms gave R and, R(free) of 12.4% and 15.0% for data to 0.91 A resolution. The hydrogen, atom on the O(gamma) atom of the reactive Ser70 is clearly seen for the, first time, bridging to the water molecule activated by Glu166. Though, hydrogen atoms on the nearby Lys73 are not seen, this observation of the, Ser70 hydrogen atom and the hydrogen bonding pattern around Lys73 indicate, that Lys73 is protonated. These findings support a role for the, Glu166-water couple, rather than Lys73, as the general base in the, deprotonation of Ser70 in the acylation process of class A, beta-lactamases. Overlay of SHV-2 with SHV-1 shows a significant 1-3 A, displacement in the 238-242 beta-strand-turn segment, making the, beta-lactam binding site more open to newer cephalosporins with large C7, substituents and thereby expanding the substrate spectrum of the variant, enzyme. The OH group of the buried Ser238 side-chain hydrogen bonds to the, main-chain CO of Asn170 on the Omega loop, that is unaltered in position, relative to SHV-1. This structural role for Ser238 in protein-protein, binding makes less likely its hydrogen bonding to oximino cephalosporins, such as cefotaxime or ceftazidime.
+Bacterial beta-lactamases hydrolyze beta-lactam antibiotics such as penicillins and cephalosporins. The TEM-type class A beta-lactamase SHV-2 is a natural variant that exhibits activity against third-generation cephalosporins normally resistant to hydrolysis by class A enzymes. SHV-2 contains a single Gly238Ser change relative to the wild-type enzyme SHV-1. Crystallographic refinement of a model including hydrogen atoms gave R and R(free) of 12.4% and 15.0% for data to 0.91 A resolution. The hydrogen atom on the O(gamma) atom of the reactive Ser70 is clearly seen for the first time, bridging to the water molecule activated by Glu166. Though hydrogen atoms on the nearby Lys73 are not seen, this observation of the Ser70 hydrogen atom and the hydrogen bonding pattern around Lys73 indicate that Lys73 is protonated. These findings support a role for the Glu166-water couple, rather than Lys73, as the general base in the deprotonation of Ser70 in the acylation process of class A beta-lactamases. Overlay of SHV-2 with SHV-1 shows a significant 1-3 A displacement in the 238-242 beta-strand-turn segment, making the beta-lactam binding site more open to newer cephalosporins with large C7 substituents and thereby expanding the substrate spectrum of the variant enzyme. The OH group of the buried Ser238 side-chain hydrogen bonds to the main-chain CO of Asn170 on the Omega loop, that is unaltered in position relative to SHV-1. This structural role for Ser238 in protein-protein binding makes less likely its hydrogen bonding to oximino cephalosporins such as cefotaxime or ceftazidime.
 ==About this Structure==
-N9B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] with MA4, EPE and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1N9B OCA].
+N9B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] with <scene name='pdbligand=MA4:'>MA4</scene>, <scene name='pdbligand=EPE:'>EPE</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1N9B OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Klebsiella pneumoniae]]
 [[Category: Single protein]]
-[[Category: Bonomo, R.A.]]
+[[Category: Bonomo, R A.]]
-[[Category: Hujer, A.M.]]
+[[Category: Hujer, A M.]]
-[[Category: Knox, J.R.]]
+[[Category: Knox, J R.]]
 [[Category: Mayama, K.]]
 [[Category: Nukaga, M.]]
@@ Line 28: / Line 28: @@
 [[Category: radiation damage]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:04:21 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:03:39 2008''