1t70

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:36, 14 February 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='1t70' size='340' side='right'caption='[[1t70]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='1t70' size='340' side='right'caption='[[1t70]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1t70]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T70 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1t70]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T70 FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mrz|1mrz]], [[1t6x|1t6x]], [[1t6y|1t6y]], [[1t6z|1t6z]], [[1t71|1t71]]</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]] 2.3&#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=1t70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t70 OCA], [http://pdbe.org/1t70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t70 RCSB], [http://www.ebi.ac.uk/pdbsum/1t70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t70 ProSAT], [http://www.topsan.org/Proteins/BSGC/1t70 TOPSAN]</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=1t70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t70 OCA], [https://pdbe.org/1t70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t70 RCSB], [https://www.ebi.ac.uk/pdbsum/1t70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t70 ProSAT], [https://www.topsan.org/Proteins/BSGC/1t70 TOPSAN]</span></td></tr>
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PPDE_DEIRA PPDE_DEIRA] Has a dual activity phosphatase/phosphodiesterase in vitro, with a preference to phosphoenolpyruvate (PEP) and 2',3'-cAMP, respectively. Can also use 2',3'-cGMP, 2',3'-cCMP and various model substrates such as p-nitrophenyl phosphate (pNPP), bis-p-nitrophenyl phosphate (bis-pNPP) and p-nitrophenyl thymidine monophosphate (pNP-TMP).<ref>PMID:17847097</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 17: Line 19:
</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=1t70 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=1t70 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
-
<div style="background-color:#fffaf0;">
 
-
== Publication Abstract from PubMed ==
 
-
We have determined the crystal structure of DR1281 from Deinococcus radiodurans. DR1281 is a protein of unknown function with over 170 homologs found in prokaryotes and eukaryotes. To elucidate the molecular function of DR1281, its crystal structure at 2.3 A resolution was determined and a series of biochemical screens for catalytic activity was performed. The crystal structure shows that DR1281 has two domains, a small alpha domain and a putative catalytic domain formed by a four-layered structure of two beta-sheets flanked by five alpha-helices on both sides. The small alpha domain interacts with other molecules in the asymmetric unit and contributes to the formation of oligomers. The structural comparison of the putative catalytic domain with known structures suggested its biochemical function to be a phosphatase, phosphodiesterase, nuclease, or nucleotidase. Structural analyses with its homologues also indicated that there is a dinuclear center at the interface of two domains formed by Asp8, Glu37, Asn38, Asn65, His148, His173, and His175. An absolute requirement of metal ions for activity has been proved by enzymatic assay with various divalent metal ions. A panel of general enzymatic assays of DR1281 revealed metal-dependent catalytic activity toward model substrates for phosphatases (p-nitrophenyl phosphate) and phosphodiesterases (bis-p-nitrophenyl phosphate). Subsequent secondary enzymatic screens with natural substrates demonstrated significant phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2',3'-cAMP. Thus, our structural and enzymatic studies have identified the biochemical function of DR1281 as a novel phosphatase/phosphodiesterase and disclosed key conserved residues involved in metal binding and catalytic activity.
 
- 
-
Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans.,Shin DH, Proudfoot M, Lim HJ, Choi IK, Yokota H, Yakunin AF, Kim R, Kim SH Proteins. 2008 Feb 15;70(3):1000-9. PMID:17847097<ref>PMID:17847097</ref>
 
- 
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
-
</div>
 
-
<div class="pdbe-citations 1t70" style="background-color:#fffaf0;"></div>
 
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Deira]]
+
[[Category: Deinococcus radiodurans R1]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Structural genomic]]
+
[[Category: Kim R]]
-
[[Category: Kim, R]]
+
[[Category: Kim SH]]
-
[[Category: Kim, S H]]
+
[[Category: Shin DH]]
-
[[Category: Shin, D H]]
+
[[Category: Wang W]]
-
[[Category: Wang, W]]
+
[[Category: Yokota H]]
-
[[Category: Yokota, H]]
+
-
[[Category: Bsgc]]
+
-
[[Category: Crystal]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Phosphatase]]
+
-
[[Category: PSI, Protein structure initiative]]
+
-
[[Category: X-ray crystallography]]
+

Current revision

Crystal structure of a novel phosphatase from Deinococcus radiodurans

PDB ID 1t70

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools