We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

1y4j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:00, 15 May 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1y4j.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of the paralogue of the human formylglycine generating enzyme==
-
|PDB= 1y4j |SIZE=350|CAPTION= <scene name='initialview01'>1y4j</scene>, resolution 1.864&Aring;
+
<StructureSection load='1y4j' size='340' side='right'caption='[[1y4j]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <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>
+
<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>
-
|ACTIVITY=
+
</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>
-
|GENE= SUMF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+
<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>
-
|DOMAIN=
+
<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>
-
|RELATEDENTRY=[[1y1e|1Y1E]], [[1y1f|1Y1F]], [[1y1g|1Y1G]], [[1y1h|1Y1H]], [[1y1i|1Y1I]], [[1y1j|1Y1J]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y4j OCA], [http://www.ebi.ac.uk/pdbsum/1y4j PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y4j RCSB]</span>
+
== 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>
-
==Overview==
+
==See Also==
-
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.
+
*[[Sulfatase-modifying factor|Sulfatase-modifying factor]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1Y4J is a [[Single protein]] structure of sequence 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].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/15687489 15687489]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Dickmanns, A.]]
+
[[Category: Dickmanns A]]
-
[[Category: Ficner, R.]]
+
[[Category: Ficner R]]
-
[[Category: Rudolph, M G.]]
+
[[Category: Rudolph MG]]
-
[[Category: duf323]]
+
-
[[Category: formylglycine]]
+
-
[[Category: homodimer]]
+
-
[[Category: multiple sulfatase deficiency]]
+
-
[[Category: sulfatase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:58:41 2008''
+

Current revision

Crystal structure of the paralogue of the human formylglycine generating enzyme

PDB ID 1y4j

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y4j"
Personal tools