1e7d: Difference between revisions
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|PDB= 1e7d |SIZE=350|CAPTION= <scene name='initialview01'>1e7d</scene>, resolution 2.80Å | |PDB= 1e7d |SIZE=350|CAPTION= <scene name='initialview01'>1e7d</scene>, resolution 2.80Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A+Putative+Active+Site+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+B+Putative+Active+Site+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Chain+A'>AC3</scene> and <scene name='pdbsite=AC4:Zn+Binding+Site+For+Chain+B'>AC4</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A+Putative+Active+Site+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Chain+B+Putative+Active+Site+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Chain+A'>AC3</scene> and <scene name='pdbsite=AC4:Zn+Binding+Site+For+Chain+B'>AC4</scene> | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= GP49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | |GENE= GP49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7d OCA], [http://www.ebi.ac.uk/pdbsum/1e7d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1e7d RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
1E7D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 1E7D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7D OCA]. | ||
==Reference== | ==Reference== | ||
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage., Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D, J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11327769 11327769] | Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage., Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D, J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11327769 11327769] | ||
[[Category: Enterobacteria phage | [[Category: Enterobacteria phage t4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Raaijmakers, H C.A.]] | [[Category: Raaijmakers, H C.A.]] | ||
| Line 26: | Line 29: | ||
[[Category: Toro, I.]] | [[Category: Toro, I.]] | ||
[[Category: Vix, O.]] | [[Category: Vix, O.]] | ||
[[Category: dnase]] | [[Category: dnase]] | ||
[[Category: endonuclease]] | [[Category: endonuclease]] | ||
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[[Category: resolvase]] | [[Category: resolvase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:56:53 2008'' | ||
Revision as of 19:56, 30 March 2008
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| , resolution 2.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | , , | ||||||
| Gene: | GP49 (Enterobacteria phage T4) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
OverviewOverview
The structure of the N62D mutant of the junction-resolving endonuclease VII (EndoVII) from phage T4 has been refined at 1.3 A, and a second wild-type crystal form solved and refined at 2.8 A resolution. Comparison of the mutant with the wild-type protein structure in two different crystal environments reveals considerable conformational flexibility at the dimer level affecting the substrate-binding cleft, the dimerization interface and the orientation of the C-terminal domains. The opening of the DNA-binding cleft, the orientation of the C-terminal domains relative to the central dimerization domain as well as the relative positioning of helices in the dimerization interface appear to be sensitive to the crystal packing environment. The highly unexpected rearrangement within the extended hydrophobic interface does change the contact surface area but keeps the number of hydrophobic contacts about the same and will therefore not require significant energy input. The conformational flexibility most likely is of functional significance for the broad substrate specificity of EndoVII. Binding of sulphate ions in the mutant structure and their positions relative to the active-site metal ions and residues known to be essential for catalysis allows us to propose a possible catalytic mechanism. A comparison with the active-site geometries of other magnesium-dependent nucleases, among them the homing endonuclease I-PpoI and Serratia endonuclease, shows common features, suggesting related catalytic mechanisms.
About this StructureAbout this Structure
1E7D is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
ReferenceReference
Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage., Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D, J Mol Biol. 2001 Apr 27;308(2):311-23. PMID:11327769
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