3o3p

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose

Structural highlights

3o3p is a 2 chain structure with sequence from Rubrobacter xylanophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.529Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B7SY86_9ACTN

Publication Abstract from PubMed

Rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (MG); moreover, the accumulation of MG is constitutive. The key enzyme for MG synthesis, catalysing the conversion of GDP-mannose (GDP-Man) and D-3-phosphoglycerate (3-PGA) into the phosphorylated intermediate mannosyl-3-phosphoglycerate and GDP, was purified from R. xylanophilus cell extracts and the corresponding gene was expressed in E. coli. Despite the related solute glucosylglycerate (GG) having never been detected in R. xylanophilus, the cell extracts and the pure recombinant mannosyl-3-phosphoglycerate synthase (MpgS) could also synthesize glucosyl-3-phosphoglycerate (GPG), the precursor of GG, in agreement with the higher homology of the novel MpgS towards GPG-synthesizing mycobacterial glucosyl-3-phosphoglycerate synthases (GpgS) than towards MpgSs from hyper/thermophiles, known to accumulate MG under salt or thermal stress. To understand the specificity and substrate ambiguity of this novel enzyme, we determined the crystal structure of the unliganded MpgS and of its complexes with the nucleotide and sugar donors, at 2.2, 2.8 and 2.5 A resolution respectively. The first three-dimensional structures of a protein from this extremely gamma-radiation-resistant thermophile here reported show that MpgS (GT81 family) contains a GT-A like fold and clearly explain its nucleotide and sugar-donor specificity. In the GDP-Man complex, a flexible loop ((254) RQNRHQ(259) ), located close to the active site moves towards the incoming sugar moiety, providing the ligands for both magnesium ion co-ordination and sugar binding. A triple mutant of R. xylanophilus MpgS, mimicking the (206) PLAGE(210) loop stabilizing hydrogen bond network observed for mycobacterial GpgSs, reduces significantly the affinity to GDP-Man, implicating this loop in the sugar-donor discrimination.

Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity.,Empadinhas N, Pereira PJ, Albuquerque L, Costa J, Sa-Moura B, Marques AT, Macedo-Ribeiro S, da Costa MS Mol Microbiol. 2011 Jan;79(1):76-93. doi:, 10.1111/j.1365-2958.2010.07432.x. Epub 2010 Nov 2. PMID:21166895^[1]

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

References

↑ Empadinhas N, Pereira PJ, Albuquerque L, Costa J, Sa-Moura B, Marques AT, Macedo-Ribeiro S, da Costa MS. Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity. Mol Microbiol. 2011 Jan;79(1):76-93. doi:, 10.1111/j.1365-2958.2010.07432.x. Epub 2010 Nov 2. PMID:21166895 doi:10.1111/j.1365-2958.2010.07432.x

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3o3p"

@@ Line 1: / Line 1: @@
-[[Image:3o3p.png|left|200px]]
-<!--
+==Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose==
-The line below this paragraph, containing "STRUCTURE_3o3p", creates the "Structure Box" on the page.
+<StructureSection load='3o3p' size='340' side='right'caption='[[3o3p]], [[Resolution|resolution]] 2.53&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3o3p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rubrobacter_xylanophilus Rubrobacter xylanophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O3P FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.529&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDD:GUANOSINE-5-DIPHOSPHATE-ALPHA-D-MANNOSE'>GDD</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3o3p|  PDB=3o3p  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o3p OCA], [https://pdbe.org/3o3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o3p RCSB], [https://www.ebi.ac.uk/pdbsum/3o3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o3p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/B7SY86_9ACTN B7SY86_9ACTN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (MG); moreover, the accumulation of MG is constitutive. The key enzyme for MG synthesis, catalysing the conversion of GDP-mannose (GDP-Man) and D-3-phosphoglycerate (3-PGA) into the phosphorylated intermediate mannosyl-3-phosphoglycerate and GDP, was purified from R. xylanophilus cell extracts and the corresponding gene was expressed in E. coli. Despite the related solute glucosylglycerate (GG) having never been detected in R. xylanophilus, the cell extracts and the pure recombinant mannosyl-3-phosphoglycerate synthase (MpgS) could also synthesize glucosyl-3-phosphoglycerate (GPG), the precursor of GG, in agreement with the higher homology of the novel MpgS towards GPG-synthesizing mycobacterial glucosyl-3-phosphoglycerate synthases (GpgS) than towards MpgSs from hyper/thermophiles, known to accumulate MG under salt or thermal stress. To understand the specificity and substrate ambiguity of this novel enzyme, we determined the crystal structure of the unliganded MpgS and of its complexes with the nucleotide and sugar donors, at 2.2, 2.8 and 2.5 A resolution respectively. The first three-dimensional structures of a protein from this extremely gamma-radiation-resistant thermophile here reported show that MpgS (GT81 family) contains a GT-A like fold and clearly explain its nucleotide and sugar-donor specificity. In the GDP-Man complex, a flexible loop ((254) RQNRHQ(259) ), located close to the active site moves towards the incoming sugar moiety, providing the ligands for both magnesium ion co-ordination and sugar binding. A triple mutant of R. xylanophilus MpgS, mimicking the (206) PLAGE(210) loop stabilizing hydrogen bond network observed for mycobacterial GpgSs, reduces significantly the affinity to GDP-Man, implicating this loop in the sugar-donor discrimination.
-===Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose===
+Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity.,Empadinhas N, Pereira PJ, Albuquerque L, Costa J, Sa-Moura B, Marques AT, Macedo-Ribeiro S, da Costa MS Mol Microbiol. 2011 Jan;79(1):76-93. doi:, 10.1111/j.1365-2958.2010.07432.x. Epub 2010 Nov 2. PMID:21166895<ref>PMID:21166895</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_21166895}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3o3p" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21166895 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21166895}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3o3p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rubrobacter_xylanophilus Rubrobacter xylanophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3P OCA].
-==Reference==
-<ref group="xtra">PMID:21166895</ref><references group="xtra"/>
-[[Category: Mannosyl-3-phosphoglycerate synthase]]
 [[Category: Rubrobacter xylanophilus]]
-[[Category: Costa, M S.da.]]
+[[Category: Empadinhas N]]
-[[Category: Empadinhas, N.]]
+[[Category: Macedo-Ribeiro S]]
-[[Category: Macedo-Ribeiro, S.]]
+[[Category: Pereira PJB]]
-[[Category: Pereira, P J.B.]]
+[[Category: Da Costa MS]]

3o3p

From Proteopedia

Current revision

Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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