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| | ==Crystal structure of the catalytic domain of LiCMS in complexed with pyruvate== | | ==Crystal structure of the catalytic domain of LiCMS in complexed with pyruvate== |
| - | <StructureSection load='3blf' size='340' side='right' caption='[[3blf]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='3blf' size='340' side='right'caption='[[3blf]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3blf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3blf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLF FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ble|3ble]], [[3bli|3bli]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cimA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans])</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=3blf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blf OCA], [https://pdbe.org/3blf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blf RCSB], [https://www.ebi.ac.uk/pdbsum/3blf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blf ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-isopropylmalate_synthase 2-isopropylmalate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.13 2.3.3.13] </span></td></tr>
| + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3blf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blf RCSB], [http://www.ebi.ac.uk/pdbsum/3blf PDBsum]</span></td></tr> | + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/CIMA_LEPIN CIMA_LEPIN] Catalyzes the condensation of pyruvate and acetyl-coenzyme A to form (R)-citramalate (PubMed:15292141, PubMed:18498255, PubMed:19351325). Shows strict substrate specificity for pyruvate. Cannot use alpha-ketoisovalerate, alpha-ketobutyrate, alpha-ketoisocaproate, alpha-ketoglutarate or glyoxylate (PubMed:15292141, PubMed:18498255).<ref>PMID:15292141</ref> <ref>PMID:18498255</ref> <ref>PMID:19351325</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blf_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blf_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3blf ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3blf" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2-isopropylmalate synthase]] | + | [[Category: Large Structures]] |
| | [[Category: Leptospira interrogans]] | | [[Category: Leptospira interrogans]] |
| - | [[Category: Ma, J.]] | + | [[Category: Ma J]] |
| - | [[Category: Zhang, P.]] | + | [[Category: Zhang P]] |
| - | [[Category: Acyltransferase]]
| + | |
| - | [[Category: Amino-acid biosynthesis]]
| + | |
| - | [[Category: Branched-chain amino acid biosynthesis]]
| + | |
| - | [[Category: Leucine biosynthesis]]
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| - | [[Category: Licmsn]]
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| - | [[Category: Substrate specificity]]
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| - | [[Category: Tim barrel]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
CIMA_LEPIN Catalyzes the condensation of pyruvate and acetyl-coenzyme A to form (R)-citramalate (PubMed:15292141, PubMed:18498255, PubMed:19351325). Shows strict substrate specificity for pyruvate. Cannot use alpha-ketoisovalerate, alpha-ketobutyrate, alpha-ketoisocaproate, alpha-ketoglutarate or glyoxylate (PubMed:15292141, PubMed:18498255).[1] [2] [3]
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
Leptospira interrogans is the causative agent for leptospirosis, a zoonotic disease of global importance. In contrast with most other micro-organisms, L. interrogans employs a pyruvate pathway to synthesize isoleucine and LiCMS (L. interrogans citramalate synthase) catalyses the first reaction of the pathway which converts pyruvate and acetyl-CoA into citramalate, thus making it an attractive target for the development of antibacterial agents. We report here the crystal structures of the catalytic domain of LiCMS and its complexes with substrates, and kinetic and mutagenesis studies of LiCMS, which together reveal the molecular basis of the high substrate specificity and the catalytic mechanism of LiCMS. The catalytic domain consists of a TIM barrel flanked by an extended C-terminal region. It forms a homodimer in the crystal structure, and the active site is located at the centre of the TIM barrel near the C-terminal ends of the beta-strands and is composed of conserved residues of the beta-strands of one subunit and the C-terminal region of the other. The substrate specificity of LiCMS towards pyruvate against other alpha-oxo acids is dictated primarily by residues Leu(81), Leu(104) and Tyr(144), which form a hydrophobic pocket to accommodate the C(2)-methyl group of pyruvate. The catalysis follows the typical aldol condensation reaction, in which Glu(146) functions as a catalytic base to activate the methyl group of acetyl-CoA to form an enolated acetyl-CoA intermediate and Arg(16) as a general acid to stabilize the intermediate.
Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans.,Ma J, Zhang P, Zhang Z, Zha M, Xu H, Zhao G, Ding J Biochem J. 2008 Oct 1;415(1):45-56. PMID:18498255[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Xu H, Zhang Y, Guo X, Ren S, Staempfli AA, Chiao J, Jiang W, Zhao G. Isoleucine biosynthesis in Leptospira interrogans serotype lai strain 56601 proceeds via a threonine-independent pathway. J Bacteriol. 2004 Aug;186(16):5400-9. PMID:15292141 doi:10.1128/JB.186.16.5400-5409.2004
- ↑ Ma J, Zhang P, Zhang Z, Zha M, Xu H, Zhao G, Ding J. Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans. Biochem J. 2008 Oct 1;415(1):45-56. PMID:18498255 doi:http://dx.doi.org/10.1042/BJ20080242
- ↑ Zhang P, Ma J, Zhang Z, Zha M, Xu H, Zhao G, Ding J. Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans. Biochem J. 2009 Jun 12;421(1):133-43. PMID:19351325 doi:10.1042/BJ20090336
- ↑ Ma J, Zhang P, Zhang Z, Zha M, Xu H, Zhao G, Ding J. Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans. Biochem J. 2008 Oct 1;415(1):45-56. PMID:18498255 doi:http://dx.doi.org/10.1042/BJ20080242
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