1xxx: Difference between revisions

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-{{Seed}}
-[[Image:1xxx.png|left|200px]]
-<!--
+==Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis==
-The line below this paragraph, containing "STRUCTURE_1xxx", creates the "Structure Box" on the page.
+<StructureSection load='1xxx' size='340' side='right'caption='[[1xxx]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1xxx]] is a 8 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=1XXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XXX FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#8491;</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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1xxx|  PDB=1xxx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xxx OCA], [https://pdbe.org/1xxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xxx RCSB], [https://www.ebi.ac.uk/pdbsum/1xxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xxx ProSAT], [https://www.topsan.org/Proteins/XMTB/1xxx TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAPA_MYCTU DAPA_MYCTU] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) (Probable).<ref>PMID:18062777</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xx/1xxx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=1xxx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of the enzyme dihydrodipicolinate synthase (KEGG entry Rv2753c, EC 4.2.1.52) from Mycobacterium tuberculosis (Mtb-DHDPS) was determined and refined at 2.28 A (1 A=0.1 nm) resolution. The asymmetric unit of the crystal contains two tetramers, each of which we propose to be the functional enzyme unit. This is supported by analytical ultracentrifugation studies, which show the enzyme to be tetrameric in solution. The structure of each subunit consists of an N-terminal (beta/alpha)(8)-barrel followed by a C-terminal alpha-helical domain. The active site comprises residues from two adjacent subunits, across an interface, and is located at the C-terminal side of the (beta/alpha)(8)-barrel domain. A comparison with the other known DHDPS structures shows that the overall architecture of the active site is largely conserved, albeit the proton relay motif comprising Tyr(143), Thr(54) and Tyr(117) appears to be disrupted. The kinetic parameters of the enzyme are reported: K(M)(ASA)=0.43+/-0.02 mM, K(M)(pyruvate)=0.17+/-0.01 mM and V(max)=4.42+/-0.08 micromol x s(-1) x mg(-1). Interestingly, the V(max) of Mtb-DHDPS is 6-fold higher than the corresponding value for Escherichia coli DHDPS, and the enzyme is insensitive to feedback inhibition by (S)-lysine. This can be explained by the three-dimensional structure, which shows that the (S)-lysine-binding site is not conserved in Mtb-DHDPS, when compared with DHDPS enzymes that are known to be inhibited by (S)-lysine. A selection of metabolites from the aspartate family of amino acids do not inhibit this enzyme. A comprehensive understanding of the structure and function of this important enzyme from the (S)-lysine biosynthesis pathway may provide the key for the design of new antibiotics to combat tuberculosis.
-===Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis===
+Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis.,Kefala G, Evans GL, Griffin MD, Devenish SR, Pearce FG, Perugini MA, Gerrard JA, Weiss MS, Dobson RC Biochem J. 2008 Apr 15;411(2):351-60. PMID:18062777<ref>PMID:18062777</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xxx" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18062777}}, adds the Publication Abstract to the page
+*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18062777 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18062777}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-XXX is a 8 chains structure of sequences 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=1XXX OCA].
-==Reference==
-<ref group="xtra">PMID:18062777</ref><references group="xtra"/>
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Mycobacterium tuberculosis]]
-[[Category: Janowski, R.]]
-[[Category: Kefala, G.]]
-[[Category: Panjikar, S.]]
-[[Category: TBSGC, TB Structural Genomics Consortium.]]
-[[Category: Weiss, M S.]]
-[[Category: Dapa]]
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Lyase]]
-[[Category: Lysine biosynthesis]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Protein structure initiative]]
+[[Category: Janowski R]]
-[[Category: Psi]]
+[[Category: Kefala G]]
-[[Category: Rv2753c]]
+[[Category: Panjikar S]]
-[[Category: Structural genomic]]
+[[Category: Weiss MS]]
-[[Category: Tb structural genomics consortium]]
-[[Category: Tbsgc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:32:46 2009''