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.

1exn

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:24, 18 November 2020

T5 5'-EXONUCLEASE

Structural highlights

1exn is a 2 chain structure with sequence from Bpt5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	D15 (BPT5)
Activity:	Exodeoxyribonuclease (lambda-induced), with EC number 3.1.11.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[EXO5_BPT5] 5'-exonucleolytic degradation of double-stranded (ds) DNA. Can also cleave bifurcated nucleic acids such as flap and pseudo-Y substrates in a structure-specific manner. This requires free 5' single-stranded (ss) ends and cleaves at the ds/ss junction. Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM.

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

THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.

A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.,Ceska TA, Sayers JR, Stier G, Suck D Nature. 1996 Jul 4;382(6586):90-3. PMID:8657312^[1]

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

References

↑ Ceska TA, Sayers JR, Stier G, Suck D. A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. Nature. 1996 Jul 4;382(6586):90-3. PMID:8657312 doi:10.1038/382090a0

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/1exn"

@@ Line 1: / Line 1: @@
 ==T5 5'-EXONUCLEASE==
-<StructureSection load='1exn' size='340' side='right' caption='[[1exn]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1exn' size='340' side='right'caption='[[1exn]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1exn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt5 Bpt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1EXN FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10726 BPT5])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn 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=1exn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exn OCA], [http://pdbe.org/1exn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1exn RCSB], [http://www.ebi.ac.uk/pdbsum/1exn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1exn ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Exonuclease|Exonuclease]]
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
 *[[Sand box 211|Sand box 211]]
 == References ==
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Bpt5]]
+[[Category: Large Structures]]
 [[Category: Ceska, T A]]
 [[Category: Sayers, J R]]

1exn

From Proteopedia

Revision as of 10:24, 18 November 2020

T5 5'-EXONUCLEASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox