This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4nyh

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:36, 1 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Orthorhombic crystal form of pir1 dual specificity phosphatase core==
==Orthorhombic crystal form of pir1 dual specificity phosphatase core==
-
<StructureSection load='4nyh' size='340' side='right' caption='[[4nyh]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+
<StructureSection load='4nyh' size='340' side='right'caption='[[4nyh]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4nyh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NYH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NYH FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4nyh]] is a 3 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=4NYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NYH FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.2&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mbb|4mbb]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DUSP11, PIR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4nyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nyh OCA], [https://pdbe.org/4nyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nyh RCSB], [https://www.ebi.ac.uk/pdbsum/4nyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nyh ProSAT]</span></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=4nyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nyh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nyh RCSB], [http://www.ebi.ac.uk/pdbsum/4nyh PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DUS11_HUMAN DUS11_HUMAN]] Possesses RNA 5'-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity. Binds to RNA. May participate in nuclear mRNA metabolism.<ref>PMID:9685386</ref>
+
[https://www.uniprot.org/uniprot/DUS11_HUMAN DUS11_HUMAN] Possesses RNA 5'-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity. Binds to RNA. May participate in nuclear mRNA metabolism.<ref>PMID:9685386</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
PIR1 is an atypical dual-specificity phosphatase (DSP) that dephosphorylates RNA with a higher specificity than phosphoproteins. Here we report the atomic structure of a catalytically inactive mutant (C152S) of the human PIR1 phosphatase core (PIR1-core, residues 29-205), refined at 1.20 A resolution. PIR1-core shares structural similarities with DSPs related to Vaccinia virus VH1 and with RNA 5'-phosphatases such as the baculovirus RNA triphosphatase and the human mRNA capping enzyme. The PIR1 active site cleft is wider and deeper than that of VH1 and contains two bound ions: a phosphate trapped above the catalytic cysteine C152 exemplifies the binding mode expected for the gamma-phosphate of RNA, and approximately 6 A away, a chloride ion coordinates the general base R158. Two residues in the PIR1 phosphate-binding loop (P-loop), a histidine (H154) downstream of C152 and an asparagine (N157) preceding R158, make close contacts with the active site phosphate, and their nonaliphatic side chains are essential for phosphatase activity in vitro. These residues are conserved in all RNA 5'-phosphatases that, analogous to PIR1, lack a "general acid" residue. Thus, a deep active site crevice, two active site ions, and conserved P-loop residues stabilizing the gamma-phosphate of RNA are defining features of atypical DSPs that specialize in dephosphorylating 5'-RNA.
+
-
 
+
-
Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase.,Sankhala RS, Lokareddy RK, Cingolani G Biochemistry. 2014 Feb 11;53(5):862-71. doi: 10.1021/bi401240x. Epub 2014 Jan 31. PMID:24447265<ref>PMID:24447265</ref>
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
==See Also==
-
</div>
+
*[[Dual specificity phosphatase 3D structures|Dual specificity phosphatase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
-
[[Category: Cingolani, G]]
+
[[Category: Large Structures]]
-
[[Category: Lokareddy, R K]]
+
[[Category: Cingolani G]]
-
[[Category: Sankhala, R S]]
+
[[Category: Lokareddy RK]]
-
[[Category: Dephosphorylation]]
+
[[Category: Sankhala RS]]
-
[[Category: Dual specificity phosphatase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nucleus]]
+
-
[[Category: P-loop]]
+
-
[[Category: Protein tyrosine phosphatase]]
+
-
[[Category: Rna-rnp complex-1]]
+

Current revision

Orthorhombic crystal form of pir1 dual specificity phosphatase core

PDB ID 4nyh

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/4nyh"
Personal tools