1y30

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(New page: 200px<br /><applet load="1y30" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y30, resolution 2.20&Aring;" /> '''X-ray crystal struct...)
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[[Image:1y30.gif|left|200px]]<br /><applet load="1y30" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1y30, resolution 2.20&Aring;" />
 
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'''X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with flavin mononucleotide at 2.2 a resolution'''<br />
 
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==Overview==
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==X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with flavin mononucleotide at 2.2 a resolution==
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The X-ray crystal structure of a conserved hypothetical protein of, molecular weight 16.3 kDa from Mycobacterium tuberculosis corresponding to, open reading frame (ORF) Rv1155 has been solved by the multiwavelength, anomalous dispersion method and refined at 1.8 A resolution. The crystal, structure revealed that Rv1155 is a dimer in the crystal and that each, monomer folds into a large and a small domain; the large domain is a, six-stranded antiparallel beta-barrel flanked by two small alpha-helices, and the small domain is a helix-loop-helix motif. The dimer interface is, formed by residues protruding primarily from five of the six beta-strands, in each subunit. Based on structural similarity and on ligand binding, it, has been established that Rv1155 is a pyridoxine 5'-phosphate oxidase, the, Escherichia coli and human counterparts of which catalyse the terminal, step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used, by many enzymes involved in amino-acid metabolism. The structures of, flavin mononucleotide (FMN) and pyridoxal 5'-phosphate (PLP) bound, separately to Rv1155 have been determined at 2.2 and 1.7 A resolution, respectively. Only one monomer binds non-covalently to one FMN molecule or, to one PLP molecule. Arg55 and Lys57 are the key residues making hydrogen, bonds and ionic interactions with the phosphate and ribose groups of the, FMN molecule, whereas Arg55 and Arg129 provide hydrogen bonds and ionic, interactions with the phosphate group of the PLP. Structural comparisons, of Rv1155 from M. tuberculosis with its E. coli and human counterparts, demonstrate that the core structure is highly conserved and the, FMN-binding site is similarly disposed in each of the structures.
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<StructureSection load='1y30' size='340' side='right'caption='[[1y30]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1y30]] 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=1Y30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y30 FirstGlance]. <br>
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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]] 2.2&#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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
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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=1y30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y30 OCA], [https://pdbe.org/1y30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y30 RCSB], [https://www.ebi.ac.uk/pdbsum/1y30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y30 ProSAT], [https://www.topsan.org/Proteins/TBSGC/1y30 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/F420R_MYCTU F420R_MYCTU] F420H(2)-dependent reductase able to catalyze the reduction of biliverdin-IXalpha to bilirubin-IXalpha in vitro. However, kinetic parameters show that it is less efficient than the biliverdin reductase Rv2074 and suggest biliverdin-IXalpha is unlikely to be the native substrate of Rv1155, which probably catalyzes the reduction of an alternative molecule in vivo (PubMed:27364382). Binds coenzyme F420, but does not bind FMN or other flavins (PubMed:25644473). Cannot use pyridoxine 5'-phosphate, pyridoxamine 5'-phosphate, pyridoxal 5'-phosphate (PLP), the anti-tuberculosis drug PA-824 or aflatoxin analogs as substrates (PubMed:25644473).<ref>PMID:25644473</ref> <ref>PMID:27364382</ref>
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y3/1y30_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1y30 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1Y30 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Y30 OCA].
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*[[Pyridoxine 5'-phosphate oxidase|Pyridoxine 5'-phosphate oxidase]]
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== References ==
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==Reference==
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<references/>
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Structures of Mycobacterium tuberculosispyridoxine 5'-phosphate oxidase and its complexes with flavin mononucleotide and pyridoxal 5'-phosphate., Biswal BK, Cherney MM, Wang M, Garen C, James MN, Acta Crystallogr D Biol Crystallogr. 2005 Nov;61(Pt 11):1492-9. Epub 2005, Oct 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16239726 16239726]
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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: Biswal BK]]
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[[Category: Biswal, B.K.]]
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[[Category: Cherney MM]]
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[[Category: Cherney, M.M.]]
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[[Category: Garen C]]
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[[Category: Garen, C.]]
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[[Category: James MN]]
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[[Category: James, M.N.]]
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[[Category: Wang M]]
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[[Category: TBSGC, TB.Structural.Genomics.Consortium.]]
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[[Category: Wang, M.]]
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[[Category: FMN]]
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[[Category: flavin mononucleotide]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: structural genomics]]
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[[Category: tb structural genomics consortium]]
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[[Category: tbsgc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:24:35 2007''
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Current revision

X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with flavin mononucleotide at 2.2 a resolution

PDB ID 1y30

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