2oxv

From Proteopedia

(Difference between revisions)

Current revision

Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.

Structural highlights

2oxv is a 2 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 1.95Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2E1_ECOLX Recognizes the double-stranded sequence GAATTC and cleaves after G-1.

Publication Abstract from PubMed

Promiscuous mutant EcoRI endonucleases bind to the canonical site GAATTC more tightly than does the wild-type endonuclease, yet cleave variant (EcoRI(*)) sites more rapidly than does wild-type. The crystal structure of the A138T promiscuous mutant homodimer in complex with a GAATTC site is nearly identical to that of the wild-type complex, except that the Thr138 side chains make packing interactions with bases in the 5'-flanking regions outside the recognition hexanucleotide while excluding two bound water molecules seen in the wild-type complex. Molecular dynamics simulations confirm exclusion of these waters. The structure and simulations suggest possible reasons why binding of the A138T protein to the GAATTC site has DeltaS degrees more favorable and DeltaH degrees less favorable than for wild-type endonuclease binding. The interactions of Thr138 with flanking bases may permit A138T, unlike wild-type enzyme, to form complexes with EcoRI(*) sites that structurally resemble the specific wild-type complex with GAATTC.

Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease.,Sapienza PJ, Rosenberg JM, Jen-Jacobson L Structure. 2007 Nov;15(11):1368-82. PMID:17997963^[1]

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

References

↑ Sapienza PJ, Rosenberg JM, Jen-Jacobson L. Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure. 2007 Nov;15(11):1368-82. PMID:17997963 doi:S0969-2126(07)00341-3

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2oxv"

Categories: Escherichia coli | Large Structures | Jen-Jacobson L | Rosenberg JM | Sapienza PJ

@@ Line 3: / Line 3: @@
 <StructureSection load='2oxv' size='340' side='right'caption='[[2oxv]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2oxv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2oxv]] is a 2 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=2OXV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXV FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ecoRIR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</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=2oxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxv OCA], [https://pdbe.org/2oxv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxv RCSB], [https://www.ebi.ac.uk/pdbsum/2oxv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/T2E1_ECOLX T2E1_ECOLX]] Recognizes the double-stranded sequence GAATTC and cleaves after G-1.
+[https://www.uniprot.org/uniprot/T2E1_ECOLX T2E1_ECOLX] Recognizes the double-stranded sequence GAATTC and cleaves after G-1.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Jen-Jacobson L]]
-[[Category: Jen-Jacobson, L]]
+[[Category: Rosenberg JM]]
-[[Category: Rosenberg, J M]]
+[[Category: Sapienza PJ]]
-[[Category: Sapienza, P J]]
-[[Category: Ecori]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Promiscuous mutant]]
-[[Category: Protein-dna interaction]]
-[[Category: Relaxed specificity mutant]]
-[[Category: Type ii restriction endonuclease]]

2oxv

From Proteopedia

Current revision

Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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