1yd3

From Proteopedia

(Difference between revisions)

Revision as of 07:07, 25 April 2018

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y43F bound to its catalytic divalent cation

Structural highlights

1yd3 is a 1 chain structure with sequence from Atcc 43589. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1ln0, 1mk0, 1kft, 1d9x, 1ycz, 1yd0, 1yd1, 1yd2, 1yd4, 1yd5, 1yd6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[UVRC_THEMA] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision (By similarity).

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

Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3' incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 A resolution, which catalyzes the 3' incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond.

Structural insights into the first incision reaction during nucleotide excision repair.,Truglio JJ, Rhau B, Croteau DL, Wang L, Skorvaga M, Karakas E, DellaVecchia MJ, Wang H, Van Houten B, Kisker C EMBO J. 2005 Mar 9;24(5):885-94. Epub 2005 Feb 3. PMID:15692561^[1]

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

References

↑ Truglio JJ, Rhau B, Croteau DL, Wang L, Skorvaga M, Karakas E, DellaVecchia MJ, Wang H, Van Houten B, Kisker C. Structural insights into the first incision reaction during nucleotide excision repair. EMBO J. 2005 Mar 9;24(5):885-94. Epub 2005 Feb 3. PMID:15692561

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/1yd3"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y43F bound to its catalytic divalent cation==
 <StructureSection load='1yd3' size='340' side='right' caption='[[1yd3]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ln0|1ln0]], [[1mk0|1mk0]], [[1kft|1kft]], [[1d9x|1d9x]], [[1ycz|1ycz]], [[1yd0|1yd0]], [[1yd1|1yd1]], [[1yd2|1yd2]], [[1yd4|1yd4]], [[1yd5|1yd5]], [[1yd6|1yd6]]</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=1yd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd3 OCA], [http://pdbe.org/1yd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd3 PDBsum]</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=1yd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd3 OCA], [http://pdbe.org/1yd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd3 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd3_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1yd3

From Proteopedia

Revision as of 07:07, 25 April 2018

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y43F bound to its catalytic divalent cation

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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