2yrf: Difference between revisions

Revision as of 09:04, 25 October 2023

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion

Structural highlights

2yrf is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MTNA_BACSU Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.

Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism.,Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science. 2003 Oct 10;302(5643):286-90. PMID:14551435 doi:10.1126/science.1086997
↑ Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H. Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism. Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470 doi:17/1/126

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OCA

[1] Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science. 2003 Oct 10;302(5643):286-90. PMID:14551435 doi:10.1126/science.1086997

[2] Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H. Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism. Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470 doi:17/1/126

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='2yrf' size='340' side='right'caption='[[2yrf]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mtnA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [https://pdbe.org/2yrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [https://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>
+[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
+[[Category: Inoue T]]
-[[Category: Inoue, T]]
+[[Category: Kai Y]]
-[[Category: Kai, Y]]
+[[Category: Matsumura H]]
-[[Category: Matsumura, H]]
+[[Category: Tamura H]]
-[[Category: Tamura, H]]
-[[Category: Isomerase]]
-[[Category: Methionine salvage pathway]]

2yrf: Difference between revisions

Revision as of 09:04, 25 October 2023

Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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