1odg

From Proteopedia

(Difference between revisions)

Current revision

Very-short-patch DNA repair endonuclease bound to its reaction product site

Structural highlights

1odg is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VSR_ECOLI Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.

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

Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.

Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.,Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:12626704^[1]

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

References

↑ Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH. Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix. Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:12626704

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/1odg"

@@ Line 3: / Line 3: @@
 <StructureSection load='1odg' size='340' side='right'caption='[[1odg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1odg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1odg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1cw0|1cw0]], [[1vsr|1vsr]]</div></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=1odg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odg OCA], [https://pdbe.org/1odg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odg RCSB], [https://www.ebi.ac.uk/pdbsum/1odg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VSR_ECOLI VSR_ECOLI]] Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.
+[https://www.uniprot.org/uniprot/VSR_ECOLI VSR_ECOLI] Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
 [[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Brown, T]]
+[[Category: Brown T]]
-[[Category: Bunting, K A]]
+[[Category: Bunting KA]]
-[[Category: Headley, A]]
+[[Category: Headley A]]
-[[Category: Pearl, L H]]
+[[Category: Pearl LH]]
-[[Category: Roe, S M]]
+[[Category: Roe SM]]
-[[Category: Savva, R]]
+[[Category: Savva R]]
-[[Category: Dna repai hydrolase]]
-[[Category: Dna repair]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Nuclease]]
-[[Category: Very short patch repair]]
-[[Category: Zinc]]

1odg

From Proteopedia

Current revision

Very-short-patch DNA repair endonuclease bound to its reaction product site

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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