2aq6: Difference between revisions

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<StructureSection load='2aq6' size='340' side='right'caption='[[2aq6]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='2aq6' size='340' side='right'caption='[[2aq6]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2aq6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AQ6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2aq6]] 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=2AQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AQ6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xxo|1xxo]], [[1y30|1y30]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RV1155 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aq6 OCA], [https://pdbe.org/2aq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aq6 RCSB], [https://www.ebi.ac.uk/pdbsum/2aq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aq6 ProSAT], [https://www.topsan.org/Proteins/TBSGC/2aq6 TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aq6 OCA], [https://pdbe.org/2aq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aq6 RCSB], [https://www.ebi.ac.uk/pdbsum/2aq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aq6 ProSAT], [https://www.topsan.org/Proteins/TBSGC/2aq6 TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/Y1155_MYCTU Y1155_MYCTU]] Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).  
[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2aq6 ConSurf].
</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=2aq6 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16239726<ref>PMID:16239726</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2aq6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Biswal, B K]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Cherney, M M]]
[[Category: Biswal BK]]
[[Category: Garen, C]]
[[Category: Cherney MM]]
[[Category: James, M N]]
[[Category: Garen C]]
[[Category: Structural genomic]]
[[Category: James MN]]
[[Category: Wang, M]]
[[Category: Wang M]]
[[Category: Oxidoreductase]]
[[Category: PSI, Protein structure initiative]]
[[Category: Pyridoxal 5'-phosphate]]
[[Category: Pyridoxine 5'-phosphate oxidase]]
[[Category: Tbsgc]]

Latest revision as of 12:13, 14 February 2024

X-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 1.7 a resolutionX-ray crystal structure of mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 1.7 a resolution

Structural highlights

2aq6 is a 2 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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).[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Mashalidis EH, Gittis AG, Tomczak A, Abell C, Barry CE 3rd, Garboczi DN. Molecular insights into the binding of coenzyme F to the conserved protein Rv1155 from Mycobacterium tuberculosis. Protein Sci. 2015 Jan 31. doi: 10.1002/pro.2645. PMID:25644473 doi:http://dx.doi.org/10.1002/pro.2645
  2. ↑ Ahmed FH, Mohamed AE, Carr PD, Lee BM, Condic-Jurkic K, O'Mara ML, Jackson CJ. Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Sci. 2016 Jul 1. doi: 10.1002/pro.2975. PMID:27364382 doi:http://dx.doi.org/10.1002/pro.2975

2aq6, resolution 1.70Å

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