1xdi

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[[Image:1xdi.gif|left|200px]]
 
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==Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis==
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The line below this paragraph, containing "STRUCTURE_1xdi", creates the "Structure Box" on the page.
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<StructureSection load='1xdi' size='340' side='right'caption='[[1xdi]], [[Resolution|resolution]] 2.81&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xdi]] is a 2 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=1XDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDI FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.81&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
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{{STRUCTURE_1xdi| PDB=1xdi | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdi OCA], [https://pdbe.org/1xdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdi RCSB], [https://www.ebi.ac.uk/pdbsum/1xdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdi ProSAT], [https://www.topsan.org/Proteins/TBSGC/1xdi TOPSAN]</span></td></tr>
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</table>
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'''Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis'''
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== Function ==
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[https://www.uniprot.org/uniprot/LPDA_MYCTU LPDA_MYCTU] May contribute to virulence by increasing resistance to reactive oxygen intermediates. It can reduce 2,6-dimethyl-1,4-benzoquinone (DMBQ), 5-hydroxy-1,4-naphthaquinone (5-HNQ) and menadione. NADPH is the physiological reductant rather than NADH.<ref>PMID:15456792</ref> <ref>PMID:17097323</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The lpdA (Rv3303c) gene from Mycobacterium tuberculosis encoding a new member of the flavoprotein disulfide reductases was expressed in Escherichia coli, and the recombinant LpdA protein was purified to homogeneity. LpdA is a homotetramer and co-purifies with one molecule of tightly but noncovalently bound FAD and NADP+ per monomer. Although annotated as a probable lipoamide dehydrogenase in M. tuberculosis, LpdA cannot catalyze reduction of lipoyl substrates, because it lacks one of two cysteine residues involved in dithiol-disulfide interchange with lipoyl substrates and a His-Glu pair involved in general acid catalysis. The crystal structure of LpdA was solved by multiple isomorphous replacement with anomalous scattering, which confirmed the absence of these catalytic residues from the active site. Although LpdA cannot catalyze reduction of disulfide-bonded substrates, it catalyzes the NAD(P)H-dependent reduction of alternative electron acceptors such as 2,6-dimethyl-1,4-benzoquinone and 5-hydroxy-1,4-naphthaquinone. Significant primary deuterium kinetic isotope effects were observed with [4S-2H]NADH establishing that the enzyme promotes transfer of the C4-proS hydride of NADH. The absence of an isotope effect with [4S-2H]NADPH, the low Km value of 0.5 microm for NADPH, and the potent inhibition of the NADH-dependent reduction of 2,6-dimethyl-1,4-benzoquinone by NADP+ (Ki approximately 6 nm) and 2'-phospho-ADP-ribose (Ki approximately 800 nm), demonstrate the high affinity of LpdA for 2'-phosphorylated nucleotides and that the physiological substrate/product pair is NADPH/NADP+ rather than NADH/NAD+. Modeling of NADP+ in the active site revealed that LpdA achieves the high specificity for NADP+ through interactions involving the 2'-phosphate of NADP+ and amino acid residues that are different from those in glutathione reductase.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdi_consurf.spt"</scriptWhenChecked>
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1XDI 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=1XDI OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Characterization of a new member of the flavoprotein disulfide reductase family of enzymes from Mycobacterium tuberculosis., Argyrou A, Vetting MW, Blanchard JS, J Biol Chem. 2004 Dec 10;279(50):52694-702. Epub 2004 Sep 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15456792 15456792]
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</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=1xdi ConSurf].
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[[Category: Mycobacterium tuberculosis]]
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<div style="clear:both"></div>
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[[Category: Single protein]]
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== References ==
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[[Category: Argyrou, A.]]
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<references/>
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[[Category: Blanchard, J S.]]
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__TOC__
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[[Category: Vetting, M W.]]
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</StructureSection>
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[[Category: Fad]]
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: Nad]]
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[[Category: Argyrou A]]
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[[Category: Nadp]]
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[[Category: Blanchard JS]]
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[[Category: Reductase]]
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[[Category: Vetting MW]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:53:27 2008''
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Current revision

Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis

PDB ID 1xdi

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