6l7s

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of FKRP in complex with Mg ion, Zinc peak data

Structural highlights

6l7s is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.41Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

FKRP_HUMAN Congenital muscular dystrophy with intellectual disability;Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2I;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease;Congenital muscular dystrophy without intellectual disability. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.

Function

FKRP_HUMAN Catalyzes the transfer of CDP-ribitol to ribitol 5-phosphate previously attached by FKTN/fukutin of to the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1) (PubMed:25279699, PubMed:26923585, PubMed:29477842). This constitutes the second step in the formation of the ribose 5-phosphate tandem repeat which links the phosphorylated O-mannosyl trisaccharide to the ligand binding moiety composed of repeats of 3-xylosyl-alpha-1,3-glucuronic acid-beta-1 (PubMed:25279699, PubMed:26923585, PubMed:29477842).^[1] ^[2] ^[3]

Publication Abstract from PubMed

alpha-Dystroglycan (alpha-DG) is a highly-glycosylated surface membrane protein. Defects in the O-mannosyl glycan of alpha-DG cause dystroglycanopathy, a group of congenital muscular dystrophies. The core M3 O-mannosyl glycan contains tandem ribitol-phosphate (RboP), a characteristic feature first found in mammals. Fukutin and fukutin-related protein (FKRP), whose mutated genes underlie dystroglycanopathy, sequentially transfer RboP from cytidine diphosphate-ribitol (CDP-Rbo) to form a tandem RboP unit in the core M3 glycan. Here, we report a series of crystal structures of FKRP with and without donor (CDP-Rbo) and/or acceptor [RboP-(phospho-)core M3 peptide] substrates. FKRP has N-terminal stem and C-terminal catalytic domains, and forms a tetramer both in crystal and in solution. In the acceptor complex, the phosphate group of RboP is recognized by the catalytic domain of one subunit, and a phosphate group on O-mannose is recognized by the stem domain of another subunit. Structure-based functional studies confirmed that the dimeric structure is essential for FKRP enzymatic activity.

Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.,Kuwabara N, Imae R, Manya H, Tanaka T, Mizuno M, Tsumoto H, Kanagawa M, Kobayashi K, Toda T, Senda T, Endo T, Kato R Nat Commun. 2020 Jan 16;11(1):303. doi: 10.1038/s41467-019-14220-z. PMID:31949166^[4]

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

References

↑ Willer T, Inamori K, Venzke D, Harvey C, Morgensen G, Hara Y, Beltran Valero de Bernabe D, Yu L, Wright KM, Campbell KP. The glucuronyltransferase B4GAT1 is required for initiation of LARGE-mediated alpha-dystroglycan functional glycosylation. Elife. 2014 Oct 3;3. doi: 10.7554/eLife.03941. PMID:25279699 doi:http://dx.doi.org/10.7554/eLife.03941
↑ Kanagawa M, Kobayashi K, Tajiri M, Manya H, Kuga A, Yamaguchi Y, Akasaka-Manya K, Furukawa JI, Mizuno M, Kawakami H, Shinohara Y, Wada Y, Endo T, Toda T. Identification of a Post-translational Modification with Ribitol-Phosphate and Its Defect in Muscular Dystrophy. Cell Rep. 2016 Mar 8;14(9):2209-2223. doi: 10.1016/j.celrep.2016.02.017. Epub, 2016 Feb 25. PMID:26923585 doi:http://dx.doi.org/10.1016/j.celrep.2016.02.017
↑ Nishihara R, Kobayashi K, Imae R, Tsumoto H, Manya H, Mizuno M, Kanagawa M, Endo T, Toda T. Cell endogenous activities of fukutin and FKRP coexist with the ribitol xylosyltransferase, TMEM5. Biochem Biophys Res Commun. 2018 Mar 18;497(4):1025-1030. doi:, 10.1016/j.bbrc.2018.02.162. PMID:29477842 doi:http://dx.doi.org/10.1016/j.bbrc.2018.02.162
↑ Kuwabara N, Imae R, Manya H, Tanaka T, Mizuno M, Tsumoto H, Kanagawa M, Kobayashi K, Toda T, Senda T, Endo T, Kato R. Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy. Nat Commun. 2020 Jan 16;11(1):303. doi: 10.1038/s41467-019-14220-z. PMID:31949166 doi:http://dx.doi.org/10.1038/s41467-019-14220-z

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6l7s"

Categories: Homo sapiens | Large Structures | Kuwabara N

@@ Line 3: / Line 3: @@
 <StructureSection load='6l7s' size='340' side='right'caption='[[6l7s]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6l7s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L7S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L7S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6l7s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L7S 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.41&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FKRP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6l7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l7s OCA], [http://pdbe.org/6l7s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l7s RCSB], [http://www.ebi.ac.uk/pdbsum/6l7s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l7s ProSAT]</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=6l7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l7s OCA], [https://pdbe.org/6l7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l7s RCSB], [https://www.ebi.ac.uk/pdbsum/6l7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l7s ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/FKRP_HUMAN FKRP_HUMAN]] Congenital muscular dystrophy with intellectual disability;Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2I;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease;Congenital muscular dystrophy without intellectual disability. The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
+[https://www.uniprot.org/uniprot/FKRP_HUMAN FKRP_HUMAN] Congenital muscular dystrophy with intellectual disability;Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2I;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease;Congenital muscular dystrophy without intellectual disability. The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/FKRP_HUMAN FKRP_HUMAN]] Catalyzes the transfer of CDP-ribitol to ribitol 5-phosphate previously attached by FKTN/fukutin of to the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1) (PubMed:25279699, PubMed:26923585, PubMed:29477842). This constitutes the second step in the formation of the ribose 5-phosphate tandem repeat which links the phosphorylated O-mannosyl trisaccharide to the ligand binding moiety composed of repeats of 3-xylosyl-alpha-1,3-glucuronic acid-beta-1 (PubMed:25279699, PubMed:26923585, PubMed:29477842).<ref>PMID:25279699</ref> <ref>PMID:26923585</ref> <ref>PMID:29477842</ref>
+[https://www.uniprot.org/uniprot/FKRP_HUMAN FKRP_HUMAN] Catalyzes the transfer of CDP-ribitol to ribitol 5-phosphate previously attached by FKTN/fukutin of to the phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-3-N-acetylglucosamine-beta-4-(phosphate-6-)mannose), a carbohydrate structure present in alpha-dystroglycan (DAG1) (PubMed:25279699, PubMed:26923585, PubMed:29477842). This constitutes the second step in the formation of the ribose 5-phosphate tandem repeat which links the phosphorylated O-mannosyl trisaccharide to the ligand binding moiety composed of repeats of 3-xylosyl-alpha-1,3-glucuronic acid-beta-1 (PubMed:25279699, PubMed:26923585, PubMed:29477842).<ref>PMID:25279699</ref> <ref>PMID:26923585</ref> <ref>PMID:29477842</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Kuwabara, N]]
+[[Category: Kuwabara N]]
-[[Category: Glycosyltranferase]]
-[[Category: Phospho ribitoyl tranferase]]
-[[Category: Transferase]]

6l7s

From Proteopedia

Current revision

Crystal structure of FKRP in complex with Mg ion, Zinc peak data

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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