2dft: Difference between revisions

Revision as of 17:58, 21 February 2008

Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution

OverviewOverview

Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts shikimate to shikimate-3-phosphate. In this work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.

About this StructureAbout this Structure

2DFT is a Single protein structure of sequence from Mycobacterium tuberculosis with , and as ligands. Active as Shikimate kinase, with EC number 2.7.1.71 Full crystallographic information is available from OCA.

ReferenceReference

Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis., Dias MV, Faim LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt 1):1-6., Epub 2006 Dec 16. PMID:17183161

Page seeded by OCA on Thu Feb 21 16:58:23 2008

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OCA

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-[[Image:2dft.jpg|left|200px]]<br /><applet load="2dft" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2dft.jpg|left|200px]]<br /><applet load="2dft" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2dft, resolution 2.80&Aring;" />
 '''Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution'''<br />
 ==Overview==
-Bacteria, fungi and plants can convert carbohydrate and, phosphoenolpyruvate into chorismate, which is the precursor of various, aromatic compounds. The seven enzymes of the shikimate pathway are, responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme, in this pathway and converts shikimate to shikimate-3-phosphate. In this, work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK), are described. It was observed that both ions and shikimate influence the, conformation of residues of the active site of MtSK. Magnesium influences, the conformation of the shikimate hydroxyl groups and the position of the, side chains of some of the residues of the active site. Chloride seems to, influence the affinity of ADP and its position in the active site and the, opening length of the LID domain. Shikimate binding causes a closing of, the LID domain and also seems to influence the crystallographic packing of, SK. The results shown here could be useful for understanding the catalytic, mechanism of SK and the role of ions in the activity of this protein.
+Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts shikimate to shikimate-3-phosphate. In this work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.
 ==About this Structure==
-DFT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with MG, CL and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DFT OCA].
+DFT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=ADP:'>ADP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFT OCA].
 ==Reference==
-Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis., Dias MV, Faim LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt, 1):1-6. Epub 2006 Dec 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17183161 17183161]
+Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis., Dias MV, Faim LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt 1):1-6., Epub 2006 Dec 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17183161 17183161]
 [[Category: Mycobacterium tuberculosis]]
 [[Category: Shikimate kinase]]
 [[Category: Single protein]]
-[[Category: Azevedo, W.F.de.]]
+[[Category: Azevedo, W F.de.]]
-[[Category: Basso, L.A.]]
+[[Category: Basso, L A.]]
-[[Category: Dias, M.V.]]
+[[Category: Dias, M V.]]
-[[Category: Faim, L.M.]]
+[[Category: Faim, L M.]]
-[[Category: Oliveira, J.S.de.]]
+[[Category: Oliveira, J S.de.]]
-[[Category: Santos, D.S.]]
+[[Category: Santos, D S.]]
-[[Category: Vasconcelos, I.B.]]
+[[Category: Vasconcelos, I B.]]
 [[Category: ADP]]
 [[Category: CL]]
@@ Line 27: / Line 27: @@
 [[Category: shikimate pathway]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:35:32 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:58:23 2008''