1w66: Difference between revisions

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-{{Seed}}
-[[Image:1w66.png|left|200px]]
-<!--
+==Structure of a lipoate-protein ligase b from Mycobacterium tuberculosis==
-The line below this paragraph, containing "STRUCTURE_1w66", creates the "Structure Box" on the page.
+<StructureSection load='1w66' size='340' side='right'caption='[[1w66]], [[Resolution|resolution]] 1.08&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'>[[1w66]] is a 1 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=1W66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W66 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]] 1.08&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DKA:DECANOIC+ACID'>DKA</scene></td></tr>
-{{STRUCTURE_1w66|  PDB=1w66  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1w66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w66 OCA], [https://pdbe.org/1w66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w66 RCSB], [https://www.ebi.ac.uk/pdbsum/1w66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w66 ProSAT], [https://www.topsan.org/Proteins/XMTB/1w66 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LIPB_MYCTU LIPB_MYCTU] Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate.[HAMAP-Rule:MF_00013]<ref>PMID:16735476</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/w6/1w66_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1w66 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Lipoic acid is essential for the activation of a number of protein complexes involved in key metabolic processes. Growth of Mycobacterium tuberculosis relies on a pathway in which the lipoate attachment group is synthesized from an endogenously produced octanoic acid moiety. In patients with multiple-drug-resistant M. tuberculosis, expression of one gene from this pathway, lipB, encoding for octanoyl-[acyl carrier protein]-protein acyltransferase is considerably up-regulated, thus making it a potential target in the search for novel antiinfectives against tuberculosis. Here we present the crystal structure of the M. tuberculosis LipB protein at atomic resolution, showing an unexpected thioether-linked active-site complex with decanoic acid. We provide evidence that the transferase functions as a cysteine/lysine dyad acyltransferase, in which two invariant residues (Lys-142 and Cys-176) are likely to function as acid/base catalysts. Analysis by MS reveals that the LipB catalytic reaction proceeds by means of an internal thioesteracyl intermediate. Structural comparison of LipB with lipoate protein ligase A indicates that, despite conserved structural and sequence active-site features in the two enzymes, 4'-phosphopantetheine-bound octanoic acid recognition is a specific property of LipB.
-===STRUCTURE OF A LIPOATE-PROTEIN LIGASE B FROM MYCOBACTERIUM TUBERCULOSIS===
+The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase.,Ma Q, Zhao X, Nasser Eddine A, Geerlof A, Li X, Cronan JE, Kaufmann SH, Wilmanns M Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8662-7. Epub 2006 May 30. PMID:16735476<ref>PMID:16735476</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16735476}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1w66" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16735476 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16735476}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-W66 is a 1 chain 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=1W66 OCA].
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Ma Q]]
-==Reference==
+[[Category: Wilmanns M]]
-The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase., Ma Q, Zhao X, Nasser Eddine A, Geerlof A, Li X, Cronan JE, Kaufmann SH, Wilmanns M, Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8662-7. Epub 2006 May 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16735476 16735476]
-[[Category: Mycobacterium tuberculosis]]
-[[Category: Ma, Q.]]
-[[Category: Wilmanns, M.]]
-[[Category: XMTB, Mycobacterium Tuberculosis Structural Proteomics Project.]]
-[[Category: Acyltransferase]]
-[[Category: Lipoate-protein ligase b]]
-[[Category: Lipoic acid]]
-[[Category: Lipoyltransferase]]
-[[Category: Mycobacterium tuberculosis structural proteomics project]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]
-[[Category: Xmtb]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 18:37:22 2008''