2g1k: Difference between revisions

Revision as of 15:38, 3 March 2021

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate at 1.75 angstrom resolution

Structural highlights

2g1k is a 1 chain structure with sequence from "bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CL, SKM, SO4
Related:	1l4u, 1l4y, 1u8a, 1we2, 1zyu
Gene:	aroK ("Bacillus tuberculosis" (Zopf 1883) Klein 1884)
Activity:	Shikimate kinase, with EC number 2.7.1.71
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

Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs, because the pathway is essential in microorganisms, plants, and parasites but absent from mammals. SK catalyzes the reaction of phosphoryl transfer from ATP to shikimic acid (SA). Since 2002, a total of 11 SK structures have been reported, but none contains either the two substrate (SA and ATP) or the two product (SA-phosphate and ADP) molecules. Here, we present three crystal structures of SK from Mycobacterium tuberculosis (MtSK), including apo-MtSK, a binary complex MtSK x SA, and the ternary complex of MtSK with SA and an ATP analogue, AMPPCP. The structures of apo-MtSK and MtSK x AMPPCP x SA make it possible to elucidate the conformational changes of MtSK upon the binding of both substrates; the structure of MtSK x AMPPCP x SA reveals interactions between the protein and gamma-phosphate which indicate dynamic roles of catalytic residues Lys15 and Arg117.

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue.,Gan J, Gu Y, Li Y, Yan H, Ji X Biochemistry. 2006 Jul 18;45(28):8539-45. PMID:16834327^[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
↑ Gan J, Gu Y, Li Y, Yan H, Ji X. Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue. Biochemistry. 2006 Jul 18;45(28):8539-45. PMID:16834327 doi:10.1021/bi0606290

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] Gan J, Gu Y, Li Y, Yan H, Ji X. Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue. Biochemistry. 2006 Jul 18;45(28):8539-45. PMID:16834327 doi:10.1021/bi0606290

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate at 1.75 angstrom resolution==
-<StructureSection load='2g1k' size='340' side='right' caption='[[2g1k]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='2g1k' size='340' side='right'caption='[[2g1k]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2g1k]] 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=2G1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G1K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2g1k]] is a 1 chain structure with sequence from [https://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=2G1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G1K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l4u|1l4u]], [[1l4y|1l4y]], [[1u8a|1u8a]], [[1we2|1we2]], [[1zyu|1zyu]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l4u|1l4u]], [[1l4y|1l4y]], [[1u8a|1u8a]], [[1we2|1we2]], [[1zyu|1zyu]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroK ([https://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='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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [https://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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g1k OCA], [http://pdbe.org/2g1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2g1k RCSB], [http://www.ebi.ac.uk/pdbsum/2g1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2g1k ProSAT]</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=2g1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g1k OCA], [https://pdbe.org/2g1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g1k RCSB], [https://www.ebi.ac.uk/pdbsum/2g1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g1k 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 38: / Line 38: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Shikimate kinase]]
 [[Category: Gan, J]]

2g1k: Difference between revisions

Revision as of 15:38, 3 March 2021

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate at 1.75 angstrom resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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