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2yf4

From Proteopedia

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Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure

Structural highlights

2yf4 is a 6 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9RS96_DEIRA

Publication Abstract from PubMed

Deinococcus radiodurans is among the very few bacterial species extremely resistant to ionizing radiation, UV light, oxidizing agents, and cycles of prolonged desiccation. The proteome of D. radiodurans reflects the evolutionary pressure exerted by chronic exposure to (nonradioactive) forms of DNA and protein damage. A clear example of this adaptation is the overrepresentation of protein families involved in the removal of non-canonical nucleoside triphosphates (NTPs) whose incorporation into nascent DNA would promote mutagenesis and DNA damage. The three-dimensional structure of the DR2231 protein has been solved at 1.80 A resolution. This protein had been classified as an all-alpha-helical MazG-like protein. The present study confirms that it holds the basic structural module characteristic of the MazG superfamily; two helices form a rigid domain, and two helices form a mobile domain and connecting loops. Contrary to what is known of MazG proteins, DR2231 protein shows a functional affinity with dUTPases. Enzymatic and isothermal calorimetry assays have demonstrated high specificity toward dUTP but an inability to hydrolyze dTTP, a typical feature of dUTPases. Co-crystallization with the product of hydrolysis, dUMP, in the presence of magnesium or manganese cations, suggests similarities with the dUTP/dUDP hydrolysis mechanism reported for dimeric dUTPases. The genome of D. radiodurans encodes for all enzymes required for dTTP synthesis from dCMP, thus bypassing the need of a dUTPase. We postulate that DR2231 protein is not essential to D. radiodurans and rather performs "house-cleaning" functions within the framework of oxidative stress response. We further propose DR2231 protein as an evolutionary precursor of dimeric dUTPases.

Structural and Functional Insights into DR2231 Protein, the MazG-like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus radiodurans.,Goncalves AM, de Sanctis D, McSweeney SM J Biol Chem. 2011 Sep 2;286(35):30691-705. Epub 2011 Jul 6. PMID:21733847^[1]

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

References

↑ Goncalves AM, de Sanctis D, McSweeney SM. Structural and Functional Insights into DR2231 Protein, the MazG-like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus radiodurans. J Biol Chem. 2011 Sep 2;286(35):30691-705. Epub 2011 Jul 6. PMID:21733847 doi:10.1074/jbc.M111.247999

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yf4"

Categories: Deinococcus radiodurans R1 | Large Structures | Goncalves AMD | McSweeney SM | DeSanctis D

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF DR2231, THE MAZG-LIKE PROTEIN FROM DEINOCOCCUS RADIODURANS, APO STRUCTURE==
-<StructureSection load='2yf4' size='340' side='right' caption='[[2yf4]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+==Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure==
+<StructureSection load='2yf4' size='340' side='right'caption='[[2yf4]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yf4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YF4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yf4]] is a 6 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=2YF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YF4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2yeu|2yeu]], [[2yf3|2yf3]], [[2yf9|2yf9]], [[2yfc|2yfc]], [[2yfd|2yfd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] </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=2yf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yf4 OCA], [https://pdbe.org/2yf4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yf4 RCSB], [https://www.ebi.ac.uk/pdbsum/2yf4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yf4 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=2yf4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yf4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yf4 RCSB], [http://www.ebi.ac.uk/pdbsum/2yf4 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RS96_DEIRA Q9RS96_DEIRA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2yf4" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deinococcus radiodurans]]
+[[Category: Deinococcus radiodurans R1]]
-[[Category: Nucleoside-triphosphate diphosphatase]]
+[[Category: Large Structures]]
-[[Category: Desanctis, D]]
+[[Category: Goncalves AMD]]
-[[Category: Goncalves, A M.D]]
+[[Category: McSweeney SM]]
-[[Category: Mcsweeney, S M]]
+[[Category: DeSanctis D]]
-[[Category: Dimeric dutpase]]
-[[Category: Hydrolase]]

2yf4

From Proteopedia

Current revision

Crystal structure of DR2231, the MazG-like protein from Deinococcus radiodurans, Apo structure

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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