1j7u: Difference between revisions

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Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Complex

OverviewOverview

3',5"-Aminoglycoside phosphotransferase type IIIa [APH(3')-IIIa] is a bacterial enzyme that confers resistance to a range of aminoglycoside antibiotics while exhibiting striking homology to eukaryotic protein kinases (ePK). The structures of APH(3')-IIIa in its apoenzyme form and in complex with the nonhydrolyzable ATP analogue AMPPNP were determined to 3.2 and 2.4 A resolution, respectively. Furthermore, refinement of the previously determined ADP complex was completed. The structure of the apoenzyme revealed alternate positioning of a flexible loop (analogous to the P-loop of ePK's), occupying part of the nucleotide-binding pocket of the enzyme. Despite structural similarity to protein kinases, there was no evidence of domain movement associated with nucleotide binding. This rigidity is due to the presence of more extensive interlobe interactions in the APH(3')-IIIa structure than in the ePK's. Differences between the ADP and AMPPNP complexes are confined to the area of the nucleotide-binding pocket. The position of conserved active site residues and magnesium ions remains unchanged, but there are differences in metal coordination between the two nucleotide complexes. Comparison of the di/triphosphate binding site of APH(3')-IIIa with that of ePK's suggests that the reaction mechanism of APH(3")-IIIa and related aminoglycoside kinases will closely resemble that of eukaryotic protein kinases. However, the orientation of the adenine ring in the binding pocket differs between APH(3')-IIIa and the ePK's by a rotation of approximately 40 degrees. This alternate binding mode is likely a conserved feature among aminoglycoside kinases and could be exploited for the structure-based drug design of compounds to combat antibiotic resistance.

About this StructureAbout this Structure

1J7U is a Single protein structure of sequence from Enterococcus faecalis with and as ligands. Active as Kanamycin kinase, with EC number 2.7.1.95 Full crystallographic information is available from OCA.

ReferenceReference

Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase., Burk DL, Hon WC, Leung AK, Berghuis AM, Biochemistry. 2001 Jul 31;40(30):8756-64. PMID:11467935

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-[[Image:1j7u.jpg|left|200px]]<br /><applet load="1j7u" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1j7u, resolution 2.40&Aring;" />
 '''Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Complex'''<br />
 ==Overview==
-',5"-Aminoglycoside phosphotransferase type IIIa [APH(3')-IIIa] is a, bacterial enzyme that confers resistance to a range of aminoglycoside, antibiotics while exhibiting striking homology to eukaryotic protein, kinases (ePK). The structures of APH(3')-IIIa in its apoenzyme form and in, complex with the nonhydrolyzable ATP analogue AMPPNP were determined to, 3.2 and 2.4 A resolution, respectively. Furthermore, refinement of the, previously determined ADP complex was completed. The structure of the, apoenzyme revealed alternate positioning of a flexible loop (analogous to, the P-loop of ePK's), occupying part of the nucleotide-binding pocket of, the enzyme. Despite structural similarity to protein kinases, there was no, evidence of domain movement associated with nucleotide binding. This, rigidity is due to the presence of more extensive interlobe interactions, in the APH(3')-IIIa structure than in the ePK's. Differences between the, ADP and AMPPNP complexes are confined to the area of the, nucleotide-binding pocket. The position of conserved active site residues, and magnesium ions remains unchanged, but there are differences in metal, coordination between the two nucleotide complexes. Comparison of the, di/triphosphate binding site of APH(3')-IIIa with that of ePK's suggests, that the reaction mechanism of APH(3")-IIIa and related aminoglycoside, kinases will closely resemble that of eukaryotic protein kinases. However, the orientation of the adenine ring in the binding pocket differs between, APH(3')-IIIa and the ePK's by a rotation of approximately 40 degrees. This, alternate binding mode is likely a conserved feature among aminoglycoside, kinases and could be exploited for the structure-based drug design of, compounds to combat antibiotic resistance.
+',5"-Aminoglycoside phosphotransferase type IIIa [APH(3')-IIIa] is a bacterial enzyme that confers resistance to a range of aminoglycoside antibiotics while exhibiting striking homology to eukaryotic protein kinases (ePK). The structures of APH(3')-IIIa in its apoenzyme form and in complex with the nonhydrolyzable ATP analogue AMPPNP were determined to 3.2 and 2.4 A resolution, respectively. Furthermore, refinement of the previously determined ADP complex was completed. The structure of the apoenzyme revealed alternate positioning of a flexible loop (analogous to the P-loop of ePK's), occupying part of the nucleotide-binding pocket of the enzyme. Despite structural similarity to protein kinases, there was no evidence of domain movement associated with nucleotide binding. This rigidity is due to the presence of more extensive interlobe interactions in the APH(3')-IIIa structure than in the ePK's. Differences between the ADP and AMPPNP complexes are confined to the area of the nucleotide-binding pocket. The position of conserved active site residues and magnesium ions remains unchanged, but there are differences in metal coordination between the two nucleotide complexes. Comparison of the di/triphosphate binding site of APH(3')-IIIa with that of ePK's suggests that the reaction mechanism of APH(3")-IIIa and related aminoglycoside kinases will closely resemble that of eukaryotic protein kinases. However, the orientation of the adenine ring in the binding pocket differs between APH(3')-IIIa and the ePK's by a rotation of approximately 40 degrees. This alternate binding mode is likely a conserved feature among aminoglycoside kinases and could be exploited for the structure-based drug design of compounds to combat antibiotic resistance.
 ==About this Structure==
-J7U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis] with MG and ANP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Kanamycin_kinase Kanamycin kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.95 2.7.1.95] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J7U OCA].
+J7U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ANP:'>ANP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Kanamycin_kinase Kanamycin kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.95 2.7.1.95] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7U OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Kanamycin kinase]]
 [[Category: Single protein]]
-[[Category: Berghuis, A.M.]]
+[[Category: Berghuis, A M.]]
-[[Category: Burk, D.L.]]
+[[Category: Burk, D L.]]
-[[Category: Hon, W.C.]]
+[[Category: Hon, W C.]]
-[[Category: Leung, A.K.W.]]
+[[Category: Leung, A K.W.]]
 [[Category: ANP]]
 [[Category: MG]]
@@ Line 24: / Line 24: @@
 [[Category: kinase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:59:58 2007''
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