1vsr

From Proteopedia

(Difference between revisions)

Current revision

VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI

Structural highlights

1vsr is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
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

Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution. The protein contains one structural zinc-binding module. Unexpectedly, its overall topology resembles members of the type II restriction endonuclease family. Subsequent mutational and biochemical analyses showed that certain elements in the catalytic site are also conserved. However, the identification of a critical histidine and evidence of an active site metal-binding coordination that is novel to endonucleases indicate a distinct catalytic mechanism.

Crystallographic and functional studies of very short patch repair endonuclease.,Tsutakawa SE, Muto T, Kawate T, Jingami H, Kunishima N, Ariyoshi M, Kohda D, Nakagawa M, Morikawa K Mol Cell. 1999 May;3(5):621-8. PMID:10360178^[1]

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

References

↑ Tsutakawa SE, Muto T, Kawate T, Jingami H, Kunishima N, Ariyoshi M, Kohda D, Nakagawa M, Morikawa K. Crystallographic and functional studies of very short patch repair endonuclease. Mol Cell. 1999 May;3(5):621-8. PMID:10360178

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/1vsr"

@@ Line 1: / Line 1: @@
 ==VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI==
-<StructureSection load='1vsr' size='340' side='right' caption='[[1vsr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1vsr' size='340' side='right'caption='[[1vsr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vsr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VSR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vsr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VSR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VSR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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>
-<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=1vsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vsr OCA], [http://pdbe.org/1vsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vsr RCSB], [http://www.ebi.ac.uk/pdbsum/1vsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vsr 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=1vsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vsr OCA], [https://pdbe.org/1vsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vsr RCSB], [https://www.ebi.ac.uk/pdbsum/1vsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vsr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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 31: / Line 31: @@
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ariyoshi, M]]
+[[Category: Large Structures]]
-[[Category: Jingami, H]]
+[[Category: Ariyoshi M]]
-[[Category: Kohda, D]]
+[[Category: Jingami H]]
-[[Category: Kunishima, N]]
+[[Category: Kohda D]]
-[[Category: Morikawa, K]]
+[[Category: Kunishima N]]
-[[Category: Muto, T]]
+[[Category: Morikawa K]]
-[[Category: Nakagawa, M]]
+[[Category: Muto T]]
-[[Category: Tsutakawa, S E]]
+[[Category: Nakagawa M]]
-[[Category: Dna repair]]
+[[Category: Tsutakawa SE]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Mismatch recognition]]

1vsr

From Proteopedia

Current revision

VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI

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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