1vcc

From Proteopedia

(Difference between revisions)

Revision as of 13:20, 13 October 2021

AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77

Structural highlights

1vcc is a 1 chain structure with sequence from Vaccw. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:	DNA topoisomerase, with EC number 5.99.1.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TOP1_VACCW] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.^[1] ^[2]

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

BACKGROUND: Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. RESULTS: The crystal structure of a 9 kDa amino-terminal fragment of vaccinia virus DNA topoisomerase I has been determined at 1.6 A resolution. The fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure. CONCLUSIONS: This is the first atomic structure of any region of a eukaryotic-like DNA topoisomerase I. It has provided insights into the structural bases of the phenotypes of some single-site mutants of the intact topoisomerase. The structure has enabled us to study the interactions within a well-folded protein fragment and the camptothecin resistance of the viral topoisomerase.

Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution.,Sharma A, Hanai R, Mondragon A Structure. 1994 Aug 15;2(8):767-77. PMID:7994576^[3]

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

References

↑ Nagarajan R, Stivers JT. Major groove interactions of vaccinia Topo I provide specificity by optimally positioning the covalent phosphotyrosine linkage. Biochemistry. 2006 May 9;45(18):5775-82. PMID:16669621 doi:http://dx.doi.org/10.1021/bi060133i
↑ Stahley MR, Stivers JT. Mechanism and specificity of DNA strand exchange catalyzed by vaccinia DNA topoisomerase type I. Biochemistry. 2010 Apr 6;49(13):2786-95. PMID:20187656 doi:10.1021/bi902204v
↑ Sharma A, Hanai R, Mondragon A. Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution. Structure. 1994 Aug 15;2(8):767-77. PMID:7994576

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/1vcc"

@@ Line 3: / Line 3: @@
 <StructureSection load='1vcc' size='340' side='right'caption='[[1vcc]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vcc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccw Vaccw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VCC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vcc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccw Vaccw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VCC FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></td></tr>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase DNA topoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.2 5.99.1.2] </span></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=1vcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcc OCA], [http://pdbe.org/1vcc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vcc RCSB], [http://www.ebi.ac.uk/pdbsum/1vcc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcc 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=1vcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vcc OCA], [https://pdbe.org/1vcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vcc RCSB], [https://www.ebi.ac.uk/pdbsum/1vcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vcc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TOP1_VACCW TOP1_VACCW]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.<ref>PMID:16669621</ref> <ref>PMID:20187656</ref>
+[[https://www.uniprot.org/uniprot/TOP1_VACCW TOP1_VACCW]] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.<ref>PMID:16669621</ref> <ref>PMID:20187656</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[Topoisomerase|Topoisomerase]]
+*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 == References ==
 <references/>

1vcc

From Proteopedia

Revision as of 13:20, 13 October 2021

AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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