1f0o: Difference between revisions

Revision as of 10:25, 21 December 2022

PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE

Structural highlights

1f0o is a 4 chain structure with sequence from Proteus vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2P2_PROHU Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.

Publication Abstract from PubMed

Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.

PvuII endonuclease contains two calcium ions in active sites.,Horton JR, Cheng X J Mol Biol. 2000 Jul 28;300(5):1049-56. PMID:10903853^[1]

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

References

↑ Horton JR, Cheng X. PvuII endonuclease contains two calcium ions in active sites. J Mol Biol. 2000 Jul 28;300(5):1049-56. PMID:10903853 doi:10.1006/jmbi.2000.3938

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Horton JR, Cheng X. PvuII endonuclease contains two calcium ions in active sites. J Mol Biol. 2000 Jul 28;300(5):1049-56. PMID:10903853 doi:10.1006/jmbi.2000.3938

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='1f0o' size='340' side='right'caption='[[1f0o]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1f0o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F0O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1f0o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F0O FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1eyu|1eyu]], [[3pyi|3pyi]], [[2pyi|2pyi]], [[1pvi|1pvi]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=1f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f0o OCA], [https://pdbe.org/1f0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f0o RCSB], [https://www.ebi.ac.uk/pdbsum/1f0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f0o ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/T2P2_PROHU T2P2_PROHU]] Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.
+[https://www.uniprot.org/uniprot/T2P2_PROHU T2P2_PROHU] Recognizes the double-stranded sequence CAGCTG and cleaves after G-3.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 29905]]
 [[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Proteus vulgaris]]
-[[Category: Cheng, X]]
+[[Category: Cheng X]]
-[[Category: Horton, J R]]
+[[Category: Horton JR]]
-[[Category: Catalytic metal visualization]]
-[[Category: Endonuclease type ii]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Protein-dna complex]]
-[[Category: Restriction enzyme]]

1f0o: Difference between revisions

Revision as of 10:25, 21 December 2022

PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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