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| - | [[Image:1rvc.gif|left|200px]] | |
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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== |
| - | The line below this paragraph, containing "STRUCTURE_1rvc", creates the "Structure Box" on the page. | + | <StructureSection load='1rvc' size='340' side='right'caption='[[1rvc]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1rvc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The August 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Restriction Enzymes'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_8 10.2210/rcsb_pdb/mom_2000_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVC FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</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> |
| - | {{STRUCTURE_1rvc| PDB=1rvc | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvc OCA], [https://pdbe.org/1rvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvc RCSB], [https://www.ebi.ac.uk/pdbsum/1rvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvc ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/T2E5_ECOLX T2E5_ECOLX] Recognizes the double-stranded sequence GATATC and cleaves after T-3. |
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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'''
| + | ==See Also== |
| - | | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | 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., & 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., & 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.
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| - | ==About this Structure==
| + | |
| - | 1RVC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The following page contains interesting information on the relation of 1RVC with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb8_1.html Restriction Enzymes]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVC OCA].
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| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/7819264 7819264]
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| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| | + | [[Category: Large Structures]] |
| | + | [[Category: RCSB PDB Molecule of the Month]] |
| | [[Category: Restriction Enzymes]] | | [[Category: Restriction Enzymes]] |
| - | [[Category: Single protein]]
| + | [[Category: Kostrewa D]] |
| - | [[Category: Kostrewa, D.]] | + | [[Category: Winkler FK]] |
| - | [[Category: Winkler, F K.]] | + | |
| - | [[Category: Protein-dna complex]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:57:14 2008''
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