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1hkw

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MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LysA)

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Retrieved from "http://52.214.119.220/wiki/index.php/1hkw"

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-[[Image:1hkw.gif|left|200px]]
- {{Structure
+==MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LysA)==
-|PDB= 1hkw |SIZE=350|CAPTION= <scene name='initialview01'>1hkw</scene>, resolution 2.80&Aring;
+<StructureSection load='1hkw' size='340' side='right'caption='[[1hkw]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE= <scene name='pdbsite=SOA:So4+Binding+Site+For+Chain+B'>SOA</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1hkw]] is a 2 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=1HKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HKW FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00278 Orn_DAP_Arg_deC], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01168 Ala_racemase_N], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0019 LysA], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00635 YBL036c_PLPDEIII]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1hkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hkw OCA], [https://pdbe.org/1hkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hkw RCSB], [https://www.ebi.ac.uk/pdbsum/1hkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hkw ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hkw OCA], [http://www.ebi.ac.uk/pdbsum/1hkw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1hkw RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/DCDA_MYCTU DCDA_MYCTU] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine (Probable). Is essential for the viability of M.tuberculosis in the host.<ref>PMID:12637582</ref>
+== Evolutionary Conservation ==
-'''MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LYSA)'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/1hkw_consurf.spt"</scriptWhenChecked>
-The Mycobacterium tuberculosis lysA gene encodes the enzyme meso-diaminopimelate decarboxylase (DAPDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme. The enzyme catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. The lysA gene of M. tuberculosis H37Rv has been established as essential for bacterial survival in immunocompromised mice, demonstrating that de novo biosynthesis of lysine is essential for in vivo viability. Drugs targeted against DAPDC could be efficient anti-tuberculosis drugs, and the three-dimensional structure of DAPDC from M. tuberculosis complexed with reaction product lysine and the ternary complex with PLP and lysine in the active site has been determined. The first structure of a DAPDC confirms its classification as a fold type III PLP-dependent enzyme. The structure shows a stable 2-fold dimer in head-to-tail arrangement of a triose-phosphate isomerase (TIM) barrel-like alpha/beta domain and a C-terminal beta sheet domain, similar to the ornithine decarboxylase (ODC) fold family. PLP is covalently bound via an internal aldimine, and residues from both domains and both subunits contribute to the binding pocket. Comparison of the structure with eukaryotic ODCs, in particular with a di-fluoromethyl ornithine (DMFO)-bound ODC from Trypanosoma bruceii, indicates that corresponding DAP-analogues might be potential inhibitors for mycobacterial DAPDCs.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-HKW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HKW OCA].
+</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=1hkw ConSurf].
+<div style="clear:both"></div>
-==Reference==
+== References ==
-Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis., Gokulan K, Rupp B, Pavelka MS Jr, Jacobs WR Jr, Sacchettini JC, J Biol Chem. 2003 May 16;278(20):18588-96. Epub 2003 Mar 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12637582 12637582]
+<references/>
-[[Category: Diaminopimelate decarboxylase]]
+__TOC__
-[[Category: Mycobacterium tuberculosis]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Gokulan, K.]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Junior, M S.Pavelka.]]
+[[Category: Gokulan K]]
-[[Category: Junior, W R.Jacobs.]]
+[[Category: Jacobs Jr WR]]
-[[Category: Rupp, B.]]
+[[Category: Pavelka Jr MS]]
-[[Category: Sacchettini, J C.]]
+[[Category: Rupp B]]
-[[Category: TBSGC, TB Structural Genomics Consortium.]]
+[[Category: Sacchettini JC]]
-[[Category: lyase,decarboxylase,diaminopimelate,dapdc,plp,lysine pathway,mycobacterium tuberculosis,lysine synthetic pathway,psi,protein structure initiative,tb structural genomics consortium,tb]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: tbsgc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:06:54 2008''

1hkw

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MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LysA)

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Evolutionary Conservation

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