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1xdi

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[[Image:1xdi.gif|left|200px]]
 
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{{Structure
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==Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis==
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|PDB= 1xdi |SIZE=350|CAPTION= <scene name='initialview01'>1xdi</scene>, resolution 2.81&Aring;
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<StructureSection load='1xdi' size='340' side='right'caption='[[1xdi]], [[Resolution|resolution]] 2.81&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>
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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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|ACTIVITY=
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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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|GENE= Rv3303c - lpdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdi OCA], [http://www.ebi.ac.uk/pdbsum/1xdi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xdi RCSB]</span>
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== Function ==
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}}
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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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'''Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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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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</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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<div style="clear:both"></div>
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==Reference==
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== References ==
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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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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: Single protein]]
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[[Category: Argyrou A]]
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[[Category: Argyrou, A.]]
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[[Category: Blanchard JS]]
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[[Category: Blanchard, J S.]]
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[[Category: Vetting MW]]
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[[Category: Vetting, M W.]]
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[[Category: fad]]
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[[Category: mycobacterium tuberculosis]]
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[[Category: nad]]
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[[Category: nadp]]
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[[Category: reductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:48:07 2008''
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Current revision

Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis

PDB ID 1xdi

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