2okn: Difference between revisions

Latest revision as of 05:24, 17 October 2024

Crystal Strcture of Human Prolidase

Structural highlights

2okn is a 2 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 2.45Å
Ligands:	MN, PI
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PEPD_HUMAN Defects in PEPD are a cause of prolidase deficiency (PD) [MIM:170100. Prolidase deficiency is an autosomal recessive disorder associated with iminodipeptiduria. The clinical phenotype includes skin ulcers, mental retardation, recurrent infections, and a characteristic facies. These features, however are incompletely penetrant and highly variable in both age of onset and severity. There is a tight linkage between the polymorphisms of prolidase and the myotonic dystrophy trait.^[1] ^[2] ^[3] ^[4]

Function

PEPD_HUMAN Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Tanoue A, Endo F, Kitano A, Matsuda I. A single nucleotide change in the prolidase gene in fibroblasts from two patients with polypeptide positive prolidase deficiency. Expression of the mutant enzyme in NIH 3T3 cells. J Clin Invest. 1990 Jul;86(1):351-5. PMID:2365824 doi:https://dx.doi.org/10.1172/JCI114708
↑ Ledoux P, Scriver C, Hechtman P. Four novel PEPD alleles causing prolidase deficiency. Am J Hum Genet. 1994 Jun;54(6):1014-21. PMID:8198124
↑ Ledoux P, Scriver CR, Hechtman P. Expression and molecular analysis of mutations in prolidase deficiency. Am J Hum Genet. 1996 Nov;59(5):1035-9. PMID:8900231
↑ Forlino A, Lupi A, Vaghi P, Icaro Cornaglia A, Calligaro A, Campari E, Cetta G. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. Hum Genet. 2002 Oct;111(4-5):314-22. Epub 2002 Aug 14. PMID:12384772 doi:10.1007/s00439-002-0792-5

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OCA

[1] Tanoue A, Endo F, Kitano A, Matsuda I. A single nucleotide change in the prolidase gene in fibroblasts from two patients with polypeptide positive prolidase deficiency. Expression of the mutant enzyme in NIH 3T3 cells. J Clin Invest. 1990 Jul;86(1):351-5. PMID:2365824 doi:https://dx.doi.org/10.1172/JCI114708

[2] Ledoux P, Scriver C, Hechtman P. Four novel PEPD alleles causing prolidase deficiency. Am J Hum Genet. 1994 Jun;54(6):1014-21. PMID:8198124

[3] Ledoux P, Scriver CR, Hechtman P. Expression and molecular analysis of mutations in prolidase deficiency. Am J Hum Genet. 1996 Nov;59(5):1035-9. PMID:8900231

[4] Forlino A, Lupi A, Vaghi P, Icaro Cornaglia A, Calligaro A, Campari E, Cetta G. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. Hum Genet. 2002 Oct;111(4-5):314-22. Epub 2002 Aug 14. PMID:12384772 doi:10.1007/s00439-002-0792-5

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-[[Image:2okn.gif|left|200px]]
- {{Structure
+==Crystal Strcture of Human Prolidase==
-|PDB= 2okn |SIZE=350|CAPTION= <scene name='initialview01'>2okn</scene>, resolution 2.450&Aring;
+<StructureSection load='2okn' size='340' side='right'caption='[[2okn]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=PI:HYDROGENPHOSPHATE ION'>PI</scene>
+<table><tr><td colspan='2'>[[2okn]] 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=2OKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OKN FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
-|GENE= PEPD, PRD ([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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PI:HYDROGENPHOSPHATE+ION'>PI</scene></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=2okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2okn OCA], [https://pdbe.org/2okn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2okn RCSB], [https://www.ebi.ac.uk/pdbsum/2okn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2okn ProSAT]</span></td></tr>
+</table>
-'''Crystal Strcture of Human Prolidase'''
+== Disease ==
+[https://www.uniprot.org/uniprot/PEPD_HUMAN PEPD_HUMAN] Defects in PEPD are a cause of prolidase deficiency (PD) [MIM:[https://omim.org/entry/170100 170100]. Prolidase deficiency is an autosomal recessive disorder associated with iminodipeptiduria. The clinical phenotype includes skin ulcers, mental retardation, recurrent infections, and a characteristic facies. These features, however are incompletely penetrant and highly variable in both age of onset and severity. There is a tight linkage between the polymorphisms of prolidase and the myotonic dystrophy trait.<ref>PMID:2365824</ref> <ref>PMID:8198124</ref> <ref>PMID:8900231</ref> <ref>PMID:12384772</ref>
+== Function ==
-==Disease==
+[https://www.uniprot.org/uniprot/PEPD_HUMAN PEPD_HUMAN] Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.
-Known disease associated with this structure: Prolidase deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=170100 170100]]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
-==About this Structure==
+Check<jmol>
-OKN 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=2OKN OCA].
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/2okn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2okn ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Xaa-Pro dipeptidase]]
+[[Category: Behlke J]]
-[[Category: Behlke, J.]]
+[[Category: Buessow K]]
-[[Category: Buessow, K.]]
+[[Category: Goetz F]]
-[[Category: Goetz, F.]]
+[[Category: Heinemann U]]
-[[Category: Heinemann, U.]]
+[[Category: Mueller U]]
-[[Category: Mueller, U.]]
+[[Category: Niesen FH]]
-[[Category: Niesen, F H.]]
+[[Category: Roske Y]]
-[[Category: PSF, Protein Structure Factory.]]
-[[Category: Roske, Y.]]
-[[Category: MN]]
-[[Category: PI]]
-[[Category: acetylation]]
-[[Category: collagen degradation]]
-[[Category: dipeptidase]]
-[[Category: disease mutation]]
-[[Category: enzyme]]
-[[Category: hydrolase]]
-[[Category: manganese]]
-[[Category: metal-binding]]
-[[Category: metalloaminopeptidase]]
-[[Category: metallocarboxypeptidase]]
-[[Category: metalloprotease]]
-[[Category: pepd gene]]
-[[Category: peptidase d]]
-[[Category: phosphorylation]]
-[[Category: polymorphism]]
-[[Category: protease]]
-[[Category: protein structure factory]]
-[[Category: psf]]
-[[Category: structural genomic]]
-[[Category: xaa-pro dipeptidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:00:54 2008''

2okn: Difference between revisions

Latest revision as of 05:24, 17 October 2024

Crystal Strcture of Human Prolidase

Structural highlights

Disease

Function

Evolutionary Conservation

References

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