5xv2: Difference between revisions

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 ==Crystal structure of Rib7 mutant D33A from Methanosarcina mazei==
-<StructureSection load='5xv2' size='340' side='right' caption='[[5xv2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5xv2' size='340' side='right'caption='[[5xv2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5xv2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5xv2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei_Go1 Methanosarcina mazei Go1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XV2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv2 OCA], [http://pdbe.org/5xv2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv2 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=5xv2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv2 OCA], [https://pdbe.org/5xv2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xv2 RCSB], [https://www.ebi.ac.uk/pdbsum/5xv2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv2 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8PYN5_METMA Q8PYN5_METMA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Archaeal/fungal Rib7 and eubacterial RibG possess a reductase domain for ribosyl reduction in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for an amino and a carbonyl group of the pyrimidine ring, respectively. Here, several crystal structures of Methanosarcina mazei Rib7 are reported at 2.27-1.95A resolution, which are the first archaeal dimeric Rib7 structures. Mutational analysis displayed that no detectable activity was observed for the Bacillus subtilis RibG K151A, K151D, and K151E mutants, and the M. mazei Rib7 D33N, D33K, and E156Q variants, while 0.1-0.6% of the activity was detected for the M. mazei Rib7 N9A, S29A, D33A, and D57N variants. Our results suggest that Lys151 in B. subtilis RibG, while Asp33 together with Arg36 in M. mazei Rib7, ensure the specific substrate recognition. Unexpectedly, an endogenous NADPH cofactor is observed in M. mazei Rib7, in which the 2'-phosphate group interacts with Ser88, and Arg91. Replacement of Ser88 with glutamate eliminates the endogenous NADPH binding and switches preference to NADH. The lower melting temperature of approximately 10 degrees C for the S88E and R91A mutants suggests that nature had evolved a tightly bound NADPH to greatly enhance the structural stability of archaeal Rib7.
+Evolution of archaeal Rib7 and eubacterial RibG reductases in riboflavin biosynthesis: Substrate specificity and cofactor preference.,Chen SC, Yen TM, Chang TH, Liaw SH Biochem Biophys Res Commun. 2018 Sep 3;503(1):195-201. doi:, 10.1016/j.bbrc.2018.06.002. Epub 2018 Jun 8. PMID:29864427<ref>PMID:29864427</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5xv2" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Chang, T H]]
+[[Category: Large Structures]]
-[[Category: Chen, S C]]
+[[Category: Methanosarcina mazei Go1]]
-[[Category: Huang, M F]]
+[[Category: Chang TH]]
-[[Category: Liaw, S H]]
+[[Category: Chen SC]]
-[[Category: Yeh, T M]]
+[[Category: Huang MF]]
-[[Category: Oxidoreductase]]
+[[Category: Liaw SH]]
-[[Category: Rib7]]
+[[Category: Yeh TM]]
-[[Category: Riboflavin biosynthesis]]