1ir6

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of exonuclease RecJ bound to manganese

Structural highlights

1ir6 is a 1 chain structure with sequence from Thermus thermophilus. 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, TOPSAN

Function

RECJ_THET8 Single-stranded-DNA-specific exonuclease acting in a 5' to 3' direction; has no detectable activity on ssRNA.^[1]

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

RecJ, a 5' to 3' exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn(2+) ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.

The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.,Yamagata A, Kakuta Y, Masui R, Fukuyama K Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:11972066^[2]

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

References

↑ Wakamatsu T, Kim K, Uemura Y, Nakagawa N, Kuramitsu S, Masui R. Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. J Biol Chem. 2011 Jan 28;286(4):2807-16. doi: 10.1074/jbc.M110.161596. Epub 2010 , Nov 18. PMID:21087930 doi:http://dx.doi.org/10.1074/jbc.M110.161596
↑ Yamagata A, Kakuta Y, Masui R, Fukuyama K. The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:11972066 doi:10.1073/pnas.092547099

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ir6"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ir6' size='340' side='right'caption='[[1ir6]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ir6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IR6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ir6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IR6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1ir6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ir6 OCA], [https://pdbe.org/1ir6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ir6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ir6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ir6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ir6 TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RECJ_THET8 RECJ_THET8] Single-stranded-DNA-specific exonuclease acting in a 5' to 3' direction; has no detectable activity on ssRNA.<ref>PMID:21087930</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
 [[Category: Large Structures]]
-[[Category: Fukuyama, K]]
+[[Category: Thermus thermophilus]]
-[[Category: Kakuta, Y]]
+[[Category: Fukuyama K]]
-[[Category: Masui, R]]
+[[Category: Kakuta Y]]
-[[Category: Structural genomic]]
+[[Category: Masui R]]
-[[Category: Yamagata, A]]
+[[Category: Yamagata A]]
-[[Category: Dna recombination]]
-[[Category: Dna repair]]
-[[Category: Hydrolase]]
-[[Category: Manganese]]
-[[Category: Nuclease]]
-[[Category: Rsgi]]
-[[Category: Single-stranded dna]]
-[[Category: Two domains interconnected by alpha-helix]]

1ir6

From Proteopedia

Current revision

Crystal structure of exonuclease RecJ bound to manganese

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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