5f84: Difference between revisions

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 ==Crystal structure of Drosophila Poglut1 (Rumi) complexed with its glycoprotein product (glucosylated EGF repeat) and UDP==
-<StructureSection load='5f84' size='340' side='right' caption='[[5f84]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='5f84' size='340' side='right'caption='[[5f84]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5f84]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F84 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5f84]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F84 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5f85|5f85]], [[5f86|5f86]], [[5f87|5f87]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">rumi, CG31152 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), F9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5f84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f84 OCA], [https://pdbe.org/5f84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f84 RCSB], [https://www.ebi.ac.uk/pdbsum/5f84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f84 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] </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=5f84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f84 OCA], [http://pdbe.org/5f84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f84 RCSB], [http://www.ebi.ac.uk/pdbsum/5f84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f84 ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[http://omim.org/entry/306900 306900]]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref>   Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide.  Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[http://omim.org/entry/300807 300807]]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/RUMI_DROME RUMI_DROME]] Protein O-glucosyltransferase. Catalyzes the reaction that attaches glucose through an O-glycosidic linkage to a conserved serine residue in epidermal growth factor-like repeats. Regulates Notch signaling by glucosylating Notch in the ER, glucosylation is required for the correct folding and cleavage of Notch.<ref>PMID:18243100</ref>  [[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.
+[https://www.uniprot.org/uniprot/RUMI_DROME RUMI_DROME] Protein O-glucosyltransferase. Catalyzes the reaction that attaches glucose through an O-glycosidic linkage to a conserved serine residue in epidermal growth factor-like repeats. Regulates Notch signaling by glucosylating Notch in the ER, glucosylation is required for the correct folding and cleavage of Notch.<ref>PMID:18243100</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 19: @@
 </div>
 <div class="pdbe-citations 5f84" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Factor IX 3D structures|Factor IX 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Coagulation factor IXa]]
+[[Category: Drosophila melanogaster]]
-[[Category: Drome]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[Category: Large Structures]]
-[[Category: Li, H L]]
+[[Category: Li HL]]
-[[Category: Yu, H J]]
+[[Category: Yu HJ]]
-[[Category: Egf repeat]]
-[[Category: Glycosyltransferase]]
-[[Category: Notch regulation]]
-[[Category: Protein o-glucosyltransferase]]
-[[Category: Transferase-hydrolase complex]]