1ygr

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the tandem phosphatase domain of RPTP CD45

Structural highlights

1ygr is a 4 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 2.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PTPRC_HUMAN T-B+ severe combined immunodeficiency due to CD45 deficiency. The disease is caused by mutations affecting the gene represented in this entry. Disease susceptibility may be associated with variations affecting the gene represented in this entry.

Function

PTPRC_HUMAN Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity).

Evolutionary Conservation

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

Publication Abstract from PubMed

CD45 is the prototypic member of transmembrane receptor-like protein tyrosine phosphatases (RPTPs) and has essential roles in immune functions. The cytoplasmic region of CD45, like many other RPTPs, contains two homologous protein tyrosine phosphatase domains, active domain 1 (D1) and catalytically impaired domain 2 (D2). Here, we report crystal structure of the cytoplasmic D1D2 segment of human CD45 in native and phosphotyrosyl peptide-bound forms. The tertiary structures of D1 and D2 are very similar, but doubly phosphorylated CD3zeta immunoreceptor tyrosine-based activation motif peptide binds only the D1 active site. The D2 "active site" deviates from the other active sites significantly to the extent that excludes any possibility of catalytic activity. The relative orientation of D1 and D2 is very similar to that observed in leukocyte common antigen-related protein with both active sites in an open conformation and is restrained through an extensive network of hydrophobic interactions, hydrogen bonds, and salt bridges. This crystal structure is incompatible with the wedge model previously suggested for CD45 regulation.

Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45.,Nam HJ, Poy F, Saito H, Frederick CA J Exp Med. 2005 Feb 7;201(3):441-52. Epub 2005 Jan 31. PMID:15684325^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nam HJ, Poy F, Saito H, Frederick CA. Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45. J Exp Med. 2005 Feb 7;201(3):441-52. Epub 2005 Jan 31. PMID:15684325 doi:10.1084/jem.20041890

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ygr"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the tandem phosphatase domain of RPTP CD45==
-<StructureSection load='1ygr' size='340' side='right' caption='[[1ygr]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1ygr' size='340' side='right'caption='[[1ygr]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ygr]] is a 4 chain structure with 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=1YGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YGR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ygr]] is a 4 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=1YGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YGR FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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]] 2.9&#8491;</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=1ygr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ygr RCSB], [http://www.ebi.ac.uk/pdbsum/1ygr PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</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=1ygr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygr OCA], [https://pdbe.org/1ygr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ygr RCSB], [https://www.ebi.ac.uk/pdbsum/1ygr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ygr ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/CD45_HUMAN CD45_HUMAN]] Defects in PTPRC are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (T(-)B(+)NK(+) SCID) [MIM:[http://omim.org/entry/608971 608971]]. A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development.<ref>PMID:11145714</ref>   Genetic variations in PTPRC are involved in multiple sclerosis susceptibility (MS) [MIM:[http://omim.org/entry/126200 126200]]. MS is a neurodegenerative disorder characterized by the gradual accumulation of focal plaques of demyelination particularly in the periventricular areas of the brain. Peripheral nerves are not affected. Onset usually in third or fourth decade with intermittent progression over an extended period. The cause is still uncertain.<ref>PMID:11101853</ref>  [[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Defects in CD247 are the cause of immunodeficiency due to defect in CD3-zeta (CD3ZID) [MIM:[http://omim.org/entry/610163 610163]]. An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens.<ref>PMID:16672702</ref>
+[https://www.uniprot.org/uniprot/PTPRC_HUMAN PTPRC_HUMAN] T-B+ severe combined immunodeficiency due to CD45 deficiency. The disease is caused by mutations affecting the gene represented in this entry.  Disease susceptibility may be associated with variations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/CD45_HUMAN CD45_HUMAN]] Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity).<ref>PMID:2845400</ref> <ref>PMID:11909961</ref>  [[http://www.uniprot.org/uniprot/CD3Z_HUMAN CD3Z_HUMAN]] Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.
+[https://www.uniprot.org/uniprot/PTPRC_HUMAN PTPRC_HUMAN] Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity).
 == 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/yg/1ygr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yg/1ygr_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1ygr ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ygr" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[CD3|CD3]]
+*[[CD3 3D structures|CD3 3D structures]]
-*[[Tyrosine phosphatase|Tyrosine phosphatase]]
+*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 40: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Frederick, C A]]
+[[Category: Large Structures]]
-[[Category: Nam, H J]]
+[[Category: Frederick CA]]
-[[Category: Poy, F]]
+[[Category: Nam HJ]]
-[[Category: Saito, H]]
+[[Category: Poy F]]
-[[Category: Cd3 zeta]]
+[[Category: Saito H]]
-[[Category: Cd45]]
-[[Category: Hydrolase]]
-[[Category: Itam]]
-[[Category: Lca]]
-[[Category: Lymphocyte activation]]
-[[Category: Protein tyrosine phosphatase]]
-[[Category: Rptp]]

1ygr

From Proteopedia

Current revision

Crystal structure of the tandem phosphatase domain of RPTP CD45

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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