1y4j: Difference between revisions

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-{{Seed}}
-[[Image:1y4j.png|left|200px]]
-<!--
+==Crystal structure of the paralogue of the human formylglycine generating enzyme==
-The line below this paragraph, containing "STRUCTURE_1y4j", creates the "Structure Box" on the page.
+<StructureSection load='1y4j' size='340' side='right'caption='[[1y4j]], [[Resolution|resolution]] 1.86&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'>[[1y4j]] is a 2 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=1Y4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y4J 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]] 1.864&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_1y4j|  PDB=1y4j  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y4j OCA], [https://pdbe.org/1y4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y4j RCSB], [https://www.ebi.ac.uk/pdbsum/1y4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y4j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUMF2_HUMAN SUMF2_HUMAN] Lacks formyl-glycine generating activity and is unable to convert newly synthesized inactive sulfatases to their active form. Inhibits the activation of sulfatases by SUMF1.<ref>PMID:12757706</ref> <ref>PMID:15708861</ref> <ref>PMID:15962010</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y4/1y4j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1y4j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In eukaryotes, sulfate esters are degraded by sulfatases, which possess a unique Calpha-formylglycine residue in their active site. The defect in post-translational formation of the Calpha-formylglycine residue causes a severe lysosomal storage disorder in humans. Recently, FGE (formylglycine-generating enzyme) has been identified as the protein required for this specific modification. Using sequence comparisons, a protein homologous to FGE was found and denoted pFGE (paralog of FGE). pFGE binds a sulfatase-derived peptide bearing the FGE recognition motif, but it lacks formylglycine-generating activity. Both proteins belong to a large family of pro- and eukaryotic proteins containing the DUF323 domain, a formylglycine-generating enzyme domain of unknown three-dimensional structure. We have crystallized the glycosylated human pFGE and determined its crystal structure at a resolution of 1.86 A. The structure reveals a novel fold, which we denote the FGE fold and which therefore serves as a paradigm for the DUF323 domain. It is characterized by an asymmetric partitioning of secondary structure elements and is stabilized by two calcium cations. A deep cleft on the surface of pFGE most likely represents the sulfatase polypeptide binding site. The asymmetric unit of the pFGE crystal contains a homodimer. The putative peptide binding site is buried between the monomers, indicating a biological significance of the dimer. The structure suggests the capability of pFGE to form a heterodimer with FGE.
-===Crystal structure of the paralogue of the human formylglycine generating enzyme===
+Crystal structure of human pFGE, the paralog of the Calpha-formylglycine-generating enzyme.,Dickmanns A, Schmidt B, Rudolph MG, Mariappan M, Dierks T, von Figura K, Ficner R J Biol Chem. 2005 Apr 15;280(15):15180-7. Epub 2005 Feb 1. PMID:15687489<ref>PMID:15687489</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1y4j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15687489}}, adds the Publication Abstract to the page
+*[[Sulfatase-modifying factor|Sulfatase-modifying factor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15687489 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15687489}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Y4J is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y4J OCA].
-==Reference==
-<ref group="xtra">PMID:15687489</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Dickmanns, A.]]
+[[Category: Large Structures]]
-[[Category: Ficner, R.]]
+[[Category: Dickmanns A]]
-[[Category: Rudolph, M G.]]
+[[Category: Ficner R]]
-[[Category: Duf323]]
+[[Category: Rudolph MG]]
-[[Category: Formylglycine]]
-[[Category: Homodimer]]
-[[Category: Multiple sulfatase deficiency]]
-[[Category: Sulfatase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:38:54 2009''