1ake: Difference between revisions

Line 1:

[[Image:1ake.gif|left|200px]]<br /><applet load="1ake" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1ake.gif|left|200px]]<br /><applet load="1ake" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1ake, resolution 2.0Å" />

'''STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE'''<br />

==Overview==

The structure of adenylate kinase from Escherichia coli ligated with the, two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate, has been determined by X-ray diffraction and refined to a resolution of, 1.9 A. The asymmetric unit of the crystals contains two copies of the, complex, the structures of which agree well with each other. One of these, copies is less well ordered in the crystals than the other, it shows, generally higher temperature factors. The molecular packing in the, crystals is discussed and correlated to crystal habit and anisotropic, X-ray diffraction. The bound inhibitor simulates well the binding of, substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of, AMP is well positioned for a nucleophilic attack on the gamma-phosphate of, ATP. The observed structure readily allows the construction of a, stabilized pentaco-ordinated transition state, as proposed for the known, in-line mechanism of the enzyme, with nucleophile and leaving group in the, apical positions of a trigonal bipyramid. The kinetic data of numerous, mutations reported in the literature are correlated with the detailed, structure of the enzyme. The mutants were classified. The concomitant, increase of the Michaelis constants for ATP and AMP in the group of, mutants that modify only the ATP-binding site cannot be explained.

The structure of adenylate kinase from Escherichia coli ligated with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate has been determined by X-ray diffraction and refined to a resolution of 1.9 A. The asymmetric unit of the crystals contains two copies of the complex, the structures of which agree well with each other. One of these copies is less well ordered in the crystals than the other, it shows generally higher temperature factors. The molecular packing in the crystals is discussed and correlated to crystal habit and anisotropic X-ray diffraction. The bound inhibitor simulates well the binding of substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of AMP is well positioned for a nucleophilic attack on the gamma-phosphate of ATP. The observed structure readily allows the construction of a stabilized pentaco-ordinated transition state, as proposed for the known in-line mechanism of the enzyme, with nucleophile and leaving group in the apical positions of a trigonal bipyramid. The kinetic data of numerous mutations reported in the literature are correlated with the detailed structure of the enzyme. The mutants were classified. The concomitant increase of the Michaelis constants for ATP and AMP in the group of mutants that modify only the ATP-binding site cannot be explained.

==About this Structure==

1AKE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with AP5 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1AKE OCA].

1AKE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=AP5:'>AP5</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKE OCA].

==Reference==

Line 14:

[[Category: Escherichia coli]]

[[Category: Single protein]]

[[Category: Mueller, C.W.]]

[[Category: Mueller, C W.]]

[[Category: Schulz, G.E.]]

[[Category: Schulz, G E.]]

[[Category: AP5]]

[[Category: transferase(phosphotransferase)]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Tue Nov 20 10~~:55:~~24 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:45:27 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1ake.gif|left|200px]]<br /><applet load="1ake" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ake.gif|left|200px]]<br /><applet load="1ake" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ake, resolution 2.0&Aring;" />
 '''STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE'''<br />
 ==Overview==
-The structure of adenylate kinase from Escherichia coli ligated with the, two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate, has been determined by X-ray diffraction and refined to a resolution of, 1.9 A. The asymmetric unit of the crystals contains two copies of the, complex, the structures of which agree well with each other. One of these, copies is less well ordered in the crystals than the other, it shows, generally higher temperature factors. The molecular packing in the, crystals is discussed and correlated to crystal habit and anisotropic, X-ray diffraction. The bound inhibitor simulates well the binding of, substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of, AMP is well positioned for a nucleophilic attack on the gamma-phosphate of, ATP. The observed structure readily allows the construction of a, stabilized pentaco-ordinated transition state, as proposed for the known, in-line mechanism of the enzyme, with nucleophile and leaving group in the, apical positions of a trigonal bipyramid. The kinetic data of numerous, mutations reported in the literature are correlated with the detailed, structure of the enzyme. The mutants were classified. The concomitant, increase of the Michaelis constants for ATP and AMP in the group of, mutants that modify only the ATP-binding site cannot be explained.
+The structure of adenylate kinase from Escherichia coli ligated with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate has been determined by X-ray diffraction and refined to a resolution of 1.9 A. The asymmetric unit of the crystals contains two copies of the complex, the structures of which agree well with each other. One of these copies is less well ordered in the crystals than the other, it shows generally higher temperature factors. The molecular packing in the crystals is discussed and correlated to crystal habit and anisotropic X-ray diffraction. The bound inhibitor simulates well the binding of substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of AMP is well positioned for a nucleophilic attack on the gamma-phosphate of ATP. The observed structure readily allows the construction of a stabilized pentaco-ordinated transition state, as proposed for the known in-line mechanism of the enzyme, with nucleophile and leaving group in the apical positions of a trigonal bipyramid. The kinetic data of numerous mutations reported in the literature are correlated with the detailed structure of the enzyme. The mutants were classified. The concomitant increase of the Michaelis constants for ATP and AMP in the group of mutants that modify only the ATP-binding site cannot be explained.
 ==About this Structure==
-AKE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with AP5 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AKE OCA].
+AKE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=AP5:'>AP5</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKE OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
-[[Category: Mueller, C.W.]]
+[[Category: Mueller, C W.]]
-[[Category: Schulz, G.E.]]
+[[Category: Schulz, G E.]]
 [[Category: AP5]]
 [[Category: transferase(phosphotransferase)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:55:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:45:27 2008''