6a27

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of PprA W183R mutant form 1

Structural highlights

6a27 is a 2 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 1.353Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPRA_DEIRA dsDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. In vitro, binds to double-stranded DNA carrying strand breaks and stimulates the DNA end-joining reaction catalyzed by DNA ligases. Thus, PprA plays a critical role in a non-homologous end-joining (NHEJ) pathway for the repair of radiation-induced DNA double-strands breaks. Cannot bind to dsDNA without strand breaks or single-stranded DNA.^[1] ^[2]

Publication Abstract from PubMed

Pleiotropic protein promoting DNA repair A (PprA) is a key protein facilitating the extreme radiation resistance of Deinococcus radiodurans. PprA is a unique protein to the genus Deinococcus and exists as an oligomer ranging from a tetramer to an approximately 100-mer depending on protein concentrations. Here, the X-ray crystal structure of PprA was determined to clarify how PprA confers radiation resistance. The tertiary structure of dimeric PprA was elucidated by using mutants obtained with random and site-directed mutagenesis methods (W183R and A139R); these mutants have disabled DNA binding and polymerization functions. Because the mutant A139R and W183R proteins have dimeric assemblies with 2 different interfaces (Interfaces 1 and 2), the linear and oligomerized PprA model was constructed as a left-handed face-to-face periodic screw structure. In addition, the linear structure in solution was confirmed by small-angle scattering experiments. The site-directed mutational analysis identified essential basic amino acids for DNA binding. These analytical data support the hypothesis that a complex assembly of PprA molecules, which are extended and have a screw structure, surrounds and stretches the DNA strand, acting as a novel guide to colocalize the DNA strands for efficient DNA repairs.-Adachi, M., Shimizu, R., Shibazaki, C., Satoh, K., Fujiwara, S., Arai, S., Narumi, I., Kuroki, R. Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans.

Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans.,Adachi M, Shimizu R, Shibazaki C, Satoh K, Fujiwara S, Arai S, Narumi I, Kuroki R FASEB J. 2018 Nov 27:fj201801506R. doi: 10.1096/fj.201801506R. PMID:30481062^[3]

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

References

↑ Tanaka M, Earl AM, Howell HA, Park MJ, Eisen JA, Peterson SN, Battista JR. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics. 2004 Sep;168(1):21-33. PMID:15454524 doi:http://dx.doi.org/10.1534/genetics.104.029249
↑ Narumi I, Satoh K, Cui S, Funayama T, Kitayama S, Watanabe H. PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol Microbiol. 2004 Oct;54(1):278-85. doi: 10.1111/j.1365-2958.2004.04272.x. PMID:15458422 doi:http://dx.doi.org/10.1111/j.1365-2958.2004.04272.x
↑ Adachi M, Shimizu R, Shibazaki C, Satoh K, Fujiwara S, Arai S, Narumi I, Kuroki R. Extended structure of pleiotropic DNA repair-promoting protein PprA from Deinococcus radiodurans. FASEB J. 2018 Nov 27:fj201801506R. doi: 10.1096/fj.201801506R. PMID:30481062 doi:http://dx.doi.org/10.1096/fj.201801506R

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/6a27"

@@ Line 3: / Line 3: @@
 <StructureSection load='6a27' size='340' side='right'caption='[[6a27]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a27]] is a 2 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=6A27 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A27 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a27]] is a 2 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=6A27 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A27 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]] 1.353&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pprA, DR_A0346 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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='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=6a27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a27 OCA], [http://pdbe.org/6a27 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a27 RCSB], [http://www.ebi.ac.uk/pdbsum/6a27 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a27 ProSAT]</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=6a27 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a27 OCA], [https://pdbe.org/6a27 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a27 RCSB], [https://www.ebi.ac.uk/pdbsum/6a27 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a27 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PPRA_DEIRA PPRA_DEIRA]] dsDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. In vitro, binds to double-stranded DNA carrying strand breaks and stimulates the DNA end-joining reaction catalyzed by DNA ligases. Thus, PprA plays a critical role in a non-homologous end-joining (NHEJ) pathway for the repair of radiation-induced DNA double-strands breaks. Cannot bind to dsDNA without strand breaks or single-stranded DNA.<ref>PMID:15454524</ref> <ref>PMID:15458422</ref>
+[https://www.uniprot.org/uniprot/PPRA_DEIRA PPRA_DEIRA] dsDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. In vitro, binds to double-stranded DNA carrying strand breaks and stimulates the DNA end-joining reaction catalyzed by DNA ligases. Thus, PprA plays a critical role in a non-homologous end-joining (NHEJ) pathway for the repair of radiation-induced DNA double-strands breaks. Cannot bind to dsDNA without strand breaks or single-stranded DNA.<ref>PMID:15454524</ref> <ref>PMID:15458422</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Deira]]
+[[Category: Deinococcus radiodurans R1]]
 [[Category: Large Structures]]
-[[Category: Adachi, M]]
+[[Category: Adachi M]]
-[[Category: Arai, S]]
+[[Category: Arai S]]
-[[Category: Kuroki, R]]
+[[Category: Kuroki R]]
-[[Category: Narumi, I]]
+[[Category: Narumi I]]
-[[Category: Satoh, K]]
+[[Category: Satoh K]]
-[[Category: Shibazaki, C]]
+[[Category: Shibazaki C]]
-[[Category: Shimizu, R]]
+[[Category: Shimizu R]]
-[[Category: Dna binding protein]]

6a27

From Proteopedia

Current revision

Crystal structure of PprA W183R mutant form 1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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