1yd2

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y19F bound to the catalytic divalent cation

Structural highlights

1yd2 is a 1 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	,
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/1yd2"

@@ Line 3: / Line 3: @@
 <StructureSection load='1yd2' size='340' side='right'caption='[[1yd2]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1yd2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1yd2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ln0|1ln0]], [[1mk0|1mk0]], [[1kft|1kft]], [[1d9x|1d9x]], [[1ycz|1ycz]], [[1yd0|1yd0]], [[1yd1|1yd1]], [[1yd3|1yd3]], [[1yd4|1yd4]], [[1yd5|1yd5]], [[1yd6|1yd6]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1yd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd2 OCA], [https://pdbe.org/1yd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/UVRC_THEMA 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).
+[https://www.uniprot.org/uniprot/UVRC_THEMA 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[UvrABC|UvrABC]]
+*[[UvrABC 3D structures|UvrABC 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
 [[Category: Large Structures]]
-[[Category: Croteau, D L]]
+[[Category: Thermotoga maritima]]
-[[Category: DellaVecchia, M J]]
+[[Category: Croteau DL]]
-[[Category: Houten, B Van]]
+[[Category: DellaVecchia MJ]]
-[[Category: Karakas, E]]
+[[Category: Karakas E]]
-[[Category: Kisker, C]]
+[[Category: Kisker C]]
-[[Category: Rhau, B]]
+[[Category: Rhau B]]
-[[Category: Skorvaga, M]]
+[[Category: Skorvaga M]]
-[[Category: Truglio, J J]]
+[[Category: Truglio JJ]]
-[[Category: Wang, H]]
+[[Category: Van Houten B]]
-[[Category: Wang, L]]
+[[Category: Wang H]]
-[[Category: Dna binding protein]]
+[[Category: Wang L]]

1yd2

From Proteopedia

Current revision

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y19F bound to the 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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