This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5eke

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:31, 5 July 2023

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (F215A mutant)

Structural highlights

5eke is a 4 chain structure with sequence from Synechocystis sp. PCC 6803 substr. Kazusa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.001Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Y501_SYNY3

Publication Abstract from PubMed

The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0A resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 A from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.,Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F Nat Commun. 2016 Jan 5;7:10175. doi: 10.1038/ncomms10175. PMID:26729507^[1]

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

References

↑ Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, Mancia F. Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis. Nat Commun. 2016 Jan 5;7:10175. doi: 10.1038/ncomms10175. PMID:26729507 doi:http://dx.doi.org/10.1038/ncomms10175

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5eke"

@@ Line 3: / Line 3: @@
 <StructureSection load='5eke' size='340' side='right'caption='[[5eke]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5eke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EKE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5eke]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EKE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 3.001&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ekp|5ekp]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sll0501 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</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=5eke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eke OCA], [https://pdbe.org/5eke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eke RCSB], [https://www.ebi.ac.uk/pdbsum/5eke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eke ProSAT]</span></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=5eke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eke OCA], [http://pdbe.org/5eke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eke RCSB], [http://www.ebi.ac.uk/pdbsum/5eke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eke ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Y501_SYNY3 Y501_SYNY3]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Syny3]]
+[[Category: Synechocystis sp. PCC 6803 substr. Kazusa]]
-[[Category: Ardiccioni, C]]
+[[Category: Ardiccioni C]]
-[[Category: Banerjee, S]]
+[[Category: Banerjee S]]
-[[Category: Clarke, O B]]
+[[Category: Clarke OB]]
-[[Category: Liu, Q]]
+[[Category: Liu Q]]
-[[Category: Mancia, F]]
+[[Category: Mancia F]]
-[[Category: NYCOMPS, New York Consortium on Membrane Protein Structure]]
+[[Category: Rajashankar KR]]
-[[Category: Rajashankar, K R]]
+[[Category: Shapiro L]]
-[[Category: Shapiro, L]]
+[[Category: Tomasek D]]
-[[Category: Tomasek, D]]
-[[Category: Bactoprenol]]
-[[Category: Enzyme]]
-[[Category: Glycosyltransferase]]
-[[Category: Membrane protein]]
-[[Category: New york consortium on membrane protein structure]]
-[[Category: Nycomp]]
-[[Category: Psi-biology]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]

5eke

From Proteopedia

Revision as of 06:31, 5 July 2023

Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (F215A mutant)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox