1m0d

From Proteopedia

(Difference between revisions)

Revision as of 08:31, 2 December 2020

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

Structural highlights

1m0d is a 4 chain structure with sequence from Bpt7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1fzr, 1m0i
Gene:	Endonuclease I (BPT7)
Activity:	Deoxyribonuclease IV (phage-T(4)-induced), with EC number 3.1.21.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ENDO_BPT7] Junction-resolving enzyme that selectively binds and cleaves four-way (Holliday) DNA junctions present after viral genomic replication. These intermediates are created during DNA repair, processing of stalled replication forks and homologous genetic recombination. Introduces two nicks on the two non-crossing strands, at 5' sides of the junction. Participates also together with gp6 in the degradation of host chromosome to provide nucleotides for phage DNA synthesis.^[1] ^[2] ^[3] ^[4]

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

T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.

Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.,Hadden JM, Declais AC, Phillips SE, Lilley DM EMBO J. 2002 Jul 1;21(13):3505-15. PMID:12093751^[5]

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

References

↑ Declais AC, Fogg JM, Freeman AD, Coste F, Hadden JM, Phillips SE, Lilley DM. The complex between a four-way DNA junction and T7 endonuclease I. EMBO J. 2003 Mar 17;22(6):1398-409. PMID:12628932 doi:http://dx.doi.org/10.1093/emboj/cdg132
↑ Freeman AD, Declais AC, Lilley DM. The importance of the N-terminus of T7 endonuclease I in the interaction with DNA junctions. J Mol Biol. 2013 Jan 23;425(2):395-410. doi: 10.1016/j.jmb.2012.11.029. Epub 2012, Dec 1. PMID:23207296 doi:http://dx.doi.org/10.1016/j.jmb.2012.11.029
↑ Panayotatos N, Fontaine A. An endonuclease specific for single-stranded DNA selectively damages the genomic DNA and induces the SOS response. J Biol Chem. 1985 Mar 10;260(5):3173-7. PMID:3972821
↑ Parkinson MJ, Lilley DM. The junction-resolving enzyme T7 endonuclease I: quaternary structure and interaction with DNA. J Mol Biol. 1997 Jul 11;270(2):169-78. PMID:9236119 doi:http://dx.doi.org/10.1006/jmbi.1997.1128
↑ Hadden JM, Declais AC, Phillips SE, Lilley DM. Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I. EMBO J. 2002 Jul 1;21(13):3505-15. PMID:12093751 doi:10.1093/emboj/cdf337

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/1m0d"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions==
-<StructureSection load='1m0d' size='340' side='right' caption='[[1m0d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1m0d' size='340' side='right'caption='[[1m0d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m0d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M0D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1m0d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M0D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1M0D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fzr|1fzr]], [[1m0i|1m0i]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fzr|1fzr]], [[1m0i|1m0i]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Endonuclease I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 BPT7])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=1m0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0d OCA], [http://pdbe.org/1m0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0d RCSB], [http://www.ebi.ac.uk/pdbsum/1m0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0d ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1m0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m0d OCA], [http://pdbe.org/1m0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m0d RCSB], [http://www.ebi.ac.uk/pdbsum/1m0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m0d ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 31: / Line 31: @@
 </div>
 <div class="pdbe-citations 1m0d" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 39: @@
 </StructureSection>
 [[Category: Bpt7]]
+[[Category: Large Structures]]
 [[Category: Declais, A C]]
 [[Category: Hadden, J M]]

1m0d

From Proteopedia

Revision as of 08:31, 2 December 2020

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

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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