2iyq: Difference between revisions

Latest revision as of 14:29, 13 December 2023

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and ADP

Structural highlights

2iyq is a 1 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	ADP, CL, SKM, TRS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AROK_MYCTU Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The catalytic turnover of shikimate and ATP into the products shikimate-3-phosphate and ADP, followed by release of ADP, was studied in the crystalline environment. Based on a comparison of the structural states before initiation of the reaction and immediately after the catalytic step, we derived a structural model of the transition state that suggests that phosphoryl transfer proceeds with inversion by an in-line associative mechanism. The random sequential binding of shikimate and nucleotides is associated with domain movements. We identified a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.

Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis.,Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD J Mol Biol. 2006 Dec 1;364(3):411-23. Epub 2006 Sep 5. PMID:17020768^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Oliveira JS, Pinto CA, Basso LA, Santos DS. Cloning and overexpression in soluble form of functional shikimate kinase and 5-enolpyruvylshikimate 3-phosphate synthase enzymes from Mycobacterium tuberculosis. Protein Expr Purif. 2001 Aug;22(3):430-5. PMID:11483005 doi:10.1006/prep.2001.1457
↑ Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol. 2006 Dec 1;364(3):411-23. Epub 2006 Sep 5. PMID:17020768 doi:10.1016/j.jmb.2006.09.001
↑ Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol. 2006 Dec 1;364(3):411-23. Epub 2006 Sep 5. PMID:17020768 doi:10.1016/j.jmb.2006.09.001

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Oliveira JS, Pinto CA, Basso LA, Santos DS. Cloning and overexpression in soluble form of functional shikimate kinase and 5-enolpyruvylshikimate 3-phosphate synthase enzymes from Mycobacterium tuberculosis. Protein Expr Purif. 2001 Aug;22(3):430-5. PMID:11483005 doi:10.1006/prep.2001.1457

[2] Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol. 2006 Dec 1;364(3):411-23. Epub 2006 Sep 5. PMID:17020768 doi:10.1016/j.jmb.2006.09.001

[3] Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol. 2006 Dec 1;364(3):411-23. Epub 2006 Sep 5. PMID:17020768 doi:10.1016/j.jmb.2006.09.001

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2iyq' size='340' side='right'caption='[[2iyq]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2iyq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IYQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2IYQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2iyq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IYQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l4u|1l4u]], [[1l4y|1l4y]], [[1u8a|1u8a]], [[1zyu|1zyu]], [[2g1j|2g1j]], [[2g1k|2g1k]], [[2iyr|2iyr]], [[2iys|2iys]], [[2iyt|2iyt]], [[2iyu|2iyu]], [[2iyv|2iyv]], [[2iyw|2iyw]], [[2iyx|2iyx]], [[2iyy|2iyy]], [[2iyz|2iyz]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2iyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iyq OCA], [https://pdbe.org/2iyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iyq RCSB], [https://www.ebi.ac.uk/pdbsum/2iyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iyq ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2iyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iyq OCA], [http://pdbe.org/2iyq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iyq RCSB], [http://www.ebi.ac.uk/pdbsum/2iyq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2iyq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AROK_MYCTU AROK_MYCTU]] Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.<ref>PMID:11483005</ref> <ref>PMID:17020768</ref>
+[https://www.uniprot.org/uniprot/AROK_MYCTU AROK_MYCTU] Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.<ref>PMID:11483005</ref> <ref>PMID:17020768</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Shikimate kinase|Shikimate kinase]]
+*[[Shikimate kinase 3D structures|Shikimate kinase 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Myctu]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Shikimate kinase]]
+[[Category: Bartunik HD]]
-[[Category: Bartunik, H D]]
+[[Category: Bourenkov GP]]
-[[Category: Bourenkov, G P]]
+[[Category: Hartmann MD]]
-[[Category: Hartmann, M D]]
+[[Category: Oberschall A]]
-[[Category: Oberschall, A]]
+[[Category: Strizhov N]]
-[[Category: Strizhov, N]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Aromatic amino acid biosynthesis]]
-[[Category: Atp-binding]]
-[[Category: Kinase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: P-loop kinase]]
-[[Category: Shikimate pathway]]
-[[Category: Transferase]]

2iyq: Difference between revisions

Latest revision as of 14:29, 13 December 2023

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and ADP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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