This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3sm4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:01, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3sm4' size='340' side='right'caption='[[3sm4]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
<StructureSection load='3sm4' size='340' side='right'caption='[[3sm4]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 1.88&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3slp|3slp]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [https://pdbe.org/3sm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [https://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 ProSAT]</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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [https://pdbe.org/3sm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [https://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD]] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.
+
[https://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The lambda exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of lambda exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of lambda exonuclease in complex with DNA at 1.88-A resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of lambda exonuclease operates not only at the level of the trimer, but also at the level of the monomer.
+
-
 
+
-
Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.,Zhang J, McCabe KA, Bell CE Proc Natl Acad Sci U S A. 2011 Jul 5. PMID:21730170<ref>PMID:21730170</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacteriophage lambda]]
+
[[Category: Escherichia virus Lambda]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Bell, C E]]
+
[[Category: Bell CE]]
-
[[Category: Zhang, J]]
+
[[Category: Zhang J]]
-
[[Category: 5'-3' dsdna exonuclease]]
+
-
[[Category: Dna repair]]
+
-
[[Category: Homologous recombination]]
+
-
[[Category: Hydrolase-dna complex]]
+
-
[[Category: Recombineering]]
+
-
[[Category: Single-strand annealing]]
+
-
[[Category: Type ii restriction endonuclease fold]]
+

Current revision

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

PDB ID 3sm4

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3sm4"
Personal tools