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==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==
==MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION==
<StructureSection load='1rvb' size='340' side='right' caption='[[1rvb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='1rvb' size='340' side='right'caption='[[1rvb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1rvb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RVB FirstGlance]. <br>
<table><tr><td colspan='2'>[[1rvb]] is a 4 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=1RVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVB FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rvb RCSB], [http://www.ebi.ac.uk/pdbsum/1rvb PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<table>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvb OCA], [https://pdbe.org/1rvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvb RCSB], [https://www.ebi.ac.uk/pdbsum/1rvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvb ProSAT]</span></td></tr>
<div style="background-color:#fffaf0;">
</table>
== Publication Abstract from PubMed ==
== Function ==
The type II restriction endonuclease EcoRV was crystallized as a complex with the substrate DNA undecamer AAAGATATCTT (recognition sequence underlined). These crystals diffract to much better resolution (2 A) than was the case for the previously reported complex with the decamer GGGATATCCC [Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., &amp; Wilson, K. S. (1993) EMBO J. 12, 1781-1795]. The crystal structure contains one dimer complex in the asymmetric unit and was solved by molecular replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile phosphodiester group and two carboxylate oxygens, one form Asp74 and one from Asp90, in its octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 A toward the Mg2+. After substrate cleavage in solution, isomorphous crystals containing the enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking. The structures have been refined to R factors of 0.16 at 2.1-2.0 A resolution maintaining very good stereochemistry. On the basis of these structures and inspired by recent kinetic data [Vipond, I. B., &amp; Halford, S. E. (1994) Biochemistry (second paper of three in this issue)], we have constructed a transition state model with two metals bound to the scissile phosphorane group.
[https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3.
 
Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution.,Kostrewa D, Winkler FK Biochemistry. 1995 Jan 17;34(2):683-96. PMID:7819264<ref>PMID:7819264</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Kostrewa, D.]]
[[Category: Large Structures]]
[[Category: Winkler, F K.]]
[[Category: Kostrewa D]]
[[Category: Hydrolase-dna complex]]
[[Category: Winkler FK]]
[[Category: Protein-dna complex]]

Latest revision as of 11:26, 14 February 2024

MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTIONMG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION

Structural highlights

1rvb is a 4 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 2.1Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2E5_ECOLX Recognizes the double-stranded sequence GATATC and cleaves after T-3.

See Also

1rvb, resolution 2.10Å

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