6fwr

From Proteopedia

(Difference between revisions)

Current revision

Structure of DinG in complex with ssDNA

Structural highlights

6fwr is a 2 chain structure with sequence from Escherichia coli and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DING_ECOLI DNA-dependent ATPase and 5'-3' DNA helicase (PubMed:12748189, PubMed:17416902). Can also unwind DNA-RNA hybrid duplexes. Is active on D-loops and R-loops, and on forked structures (PubMed:17416902). May be involved in recombinational DNA repair and the resumption of replication after DNA damage (PubMed:17416902). The redox cluster is involved in DNA-mediated charge-transport signaling between DNA repair proteins from distinct pathways. DinG cooperates at long-range with endonuclease III, a base excision repair enzyme, using DNA charge transport to redistribute to regions of DNA damage (PubMed:24738733).^[1] ^[2] ^[3]

Publication Abstract from PubMed

The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily 2 helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability. Consequently, mutations in several of these family members in eukaryotes cause human diseases. Family members in bacteria, such as the DinG helicase from Escherichia coli, are also involved in DNA repair. Here we present crystal structures of complexes of DinG bound to single-stranded DNA (ssDNA) in the presence and absence of an ATP analogue (ADP*BeF3), that suggest a mechanism for 5'-3' translocation along the ssDNA substrate. This proposed mechanism has implications for how those enzymes of the XPD family that recognise bulky DNA lesionsmight stall at these as the first step in initiating DNA repair. Biochemical data reveal roles for conserved residues that are mutated in human diseases.

DNA translocation mechanism of an XPD family helicase.,Cheng K, Wigley DB Elife. 2018 Dec 6;7. pii: 42400. doi: 10.7554/eLife.42400. PMID:30520735^[4]

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

References

↑ Voloshin ON, Vanevski F, Khil PP, Camerini-Otero RD. Characterization of the DNA damage-inducible helicase DinG from Escherichia coli. J Biol Chem. 2003 Jul 25;278(30):28284-93. PMID:12748189 doi:10.1074/jbc.M301188200
↑ Voloshin ON, Camerini-Otero RD. The DinG protein from Escherichia coli is a structure-specific helicase. J Biol Chem. 2007 Jun 22;282(25):18437-18447. PMID:17416902 doi:10.1074/jbc.M700376200
↑ Grodick MA, Segal HM, Zwang TJ, Barton JK. DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrity. J Am Chem Soc. 2014 Apr 30;136(17):6470-8. PMID:24738733 doi:10.1021/ja501973c
↑ Cheng K, Wigley DB. DNA translocation mechanism of an XPD family helicase. Elife. 2018 Dec 6;7. pii: 42400. doi: 10.7554/eLife.42400. PMID:30520735 doi:http://dx.doi.org/10.7554/eLife.42400

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6fwr"

Categories: Escherichia coli | Large Structures | Synthetic construct | Cheng K | Wigley DB

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6fwr is ON HOLD
+==Structure of DinG in complex with ssDNA==
+<StructureSection load='6fwr' size='340' side='right'caption='[[6fwr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6fwr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FWR FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6fwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fwr OCA], [https://pdbe.org/6fwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fwr RCSB], [https://www.ebi.ac.uk/pdbsum/6fwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fwr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DING_ECOLI DING_ECOLI] DNA-dependent ATPase and 5'-3' DNA helicase (PubMed:12748189, PubMed:17416902). Can also unwind DNA-RNA hybrid duplexes. Is active on D-loops and R-loops, and on forked structures (PubMed:17416902). May be involved in recombinational DNA repair and the resumption of replication after DNA damage (PubMed:17416902). The redox cluster is involved in DNA-mediated charge-transport signaling between DNA repair proteins from distinct pathways. DinG cooperates at long-range with endonuclease III, a base excision repair enzyme, using DNA charge transport to redistribute to regions of DNA damage (PubMed:24738733).<ref>PMID:12748189</ref> <ref>PMID:17416902</ref> <ref>PMID:24738733</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily 2 helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability. Consequently, mutations in several of these family members in eukaryotes cause human diseases. Family members in bacteria, such as the DinG helicase from Escherichia coli, are also involved in DNA repair. Here we present crystal structures of complexes of DinG bound to single-stranded DNA (ssDNA) in the presence and absence of an ATP analogue (ADP*BeF3), that suggest a mechanism for 5'-3' translocation along the ssDNA substrate. This proposed mechanism has implications for how those enzymes of the XPD family that recognise bulky DNA lesionsmight stall at these as the first step in initiating DNA repair. Biochemical data reveal roles for conserved residues that are mutated in human diseases.
-Authors:
+DNA translocation mechanism of an XPD family helicase.,Cheng K, Wigley DB Elife. 2018 Dec 6;7. pii: 42400. doi: 10.7554/eLife.42400. PMID:30520735<ref>PMID:30520735</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6fwr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Cheng K]]
+[[Category: Wigley DB]]

6fwr

From Proteopedia

Current revision

Structure of DinG in complex with ssDNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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