2okn: Difference between revisions

Revision as of 10:41, 30 August 2023

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

Proteopedia Page Contributors and Editors (what is this?)

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 3: / Line 3: @@
 <StructureSection load='2okn' size='340' side='right'caption='[[2okn]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2okn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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>
+<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>
-</td></tr><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>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2iw2|2iw2]]</div></td></tr>
+<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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PEPD, PRD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=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>
 == 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>
+[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 ==
-[[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.
+[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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[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: 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: Protease]]
-[[Category: Protein structure factory]]
-[[Category: Psf]]
-[[Category: Structural genomic]]
-[[Category: Xaa-pro dipeptidase]]

2okn: Difference between revisions

Revision as of 10:41, 30 August 2023

Crystal Strcture of Human Prolidase

Structural highlights

Disease

Function

Evolutionary Conservation

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools