1u8a: Difference between revisions

Latest revision as of 06:39, 23 August 2023

Crystal Structure of Mycobacterium Tuberculosis Shikimate Kinase in Complex with Shikimate and ADP at 2.15 Angstrom Resolution

Structural highlights

1u8a is a 1 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:	ADP, CL, SKM
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 X-ray crystal structure of Mycobacterium tuberculosis shikimate kinase (SK) with bound shikimate and adenosine diphosphate (ADP) has been determined to a resolution of 2.15 A. The binding of shikimate in a shikimate kinase crystal structure has not previously been reported. The substrate binds in a pocket lined with hydrophobic residues and interacts with several highly conserved charged residues including Asp34, Arg58, Glu61 and Arg136 which project into the cavity. Comparisons of our ternary SK-ADP-shikimate complex with an earlier binary SK-ADP complex show that conformational changes occur on shikimate binding with the substrate-binding domain rotating by 10 degrees. Detailed knowledge of shikimate binding is an important step in the design of inhibitors of SK, which have potential as novel anti-tuberculosis agents.

Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase.,Dhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK FEBS Lett. 2004 Sep 10;574(1-3):49-54. PMID:15358538^[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
↑ Dhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase. FEBS Lett. 2004 Sep 10;574(1-3):49-54. PMID:15358538 doi:10.1016/j.febslet.2004.08.005

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] Dhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase. FEBS Lett. 2004 Sep 10;574(1-3):49-54. PMID:15358538 doi:10.1016/j.febslet.2004.08.005

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='1u8a' size='340' side='right'caption='[[1u8a]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1u8a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U8A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U8A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1u8a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U8A 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></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]] 2.15&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l4y|1l4y]], [[1l4u|1l4u]]</div></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></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1u8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u8a OCA], [https://pdbe.org/1u8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u8a RCSB], [https://www.ebi.ac.uk/pdbsum/1u8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u8a ProSAT]</span></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'>[http://proteopedia.org/fgij/fg.htm?mol=1u8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u8a OCA], [http://pdbe.org/1u8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u8a RCSB], [http://www.ebi.ac.uk/pdbsum/1u8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u8a 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 33: / Line 31: @@
 ==See Also==
-*[[Shikimate kinase|Shikimate kinase]]
+*[[Shikimate kinase 3D structures|Shikimate kinase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Shikimate kinase]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: Charles, I]]
+[[Category: Charles I]]
-[[Category: Dhaliwal, B]]
+[[Category: Dhaliwal B]]
-[[Category: Hawkins, A R]]
+[[Category: Hawkins AR]]
-[[Category: Lockyer, M]]
+[[Category: Lockyer M]]
-[[Category: Nichols, C E]]
+[[Category: Nichols CE]]
-[[Category: Ren, J]]
+[[Category: Ren J]]
-[[Category: Stammers, D K]]
+[[Category: Stammers DK]]
-[[Category: Phorsphoryl transfer]]
-[[Category: Drug design]]
-[[Category: Shikimate pathway]]
-[[Category: Transferase]]

1u8a: Difference between revisions

Latest revision as of 06:39, 23 August 2023

Crystal Structure of Mycobacterium Tuberculosis Shikimate Kinase in Complex with Shikimate and ADP at 2.15 Angstrom Resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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