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.

4uob

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:29, 29 March 2023

Crystal structure of Deinococcus radiodurans Endonuclease III-3

Structural highlights

4uob is a 1 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9RVU4_DEIRA

Publication Abstract from PubMed

While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Delta76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all alpha-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity.

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.,Sarre A, Okvist M, Klar T, Hall DR, Smalas AO, McSweeney S, Timmins J, Moe E J Struct Biol. 2015 Jul 11. pii: S1047-8477(15)00138-0. doi:, 10.1016/j.jsb.2015.05.009. PMID:26172070^[1]

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

References

↑ Sarre A, Okvist M, Klar T, Hall DR, Smalas AO, McSweeney S, Timmins J, Moe E. Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans. J Struct Biol. 2015 Jul 11. pii: S1047-8477(15)00138-0. doi:, 10.1016/j.jsb.2015.05.009. PMID:26172070 doi:http://dx.doi.org/10.1016/j.jsb.2015.05.009

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/4uob"

@@ Line 3: / Line 3: @@
 <StructureSection load='4uob' size='340' side='right'caption='[[4uob]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4uob]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UOB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4uob]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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">[[4unf|4unf]]</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=4uob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uob OCA], [https://pdbe.org/4uob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uob RCSB], [https://www.ebi.ac.uk/pdbsum/4uob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uob ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=4uob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uob OCA], [http://pdbe.org/4uob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4uob RCSB], [http://www.ebi.ac.uk/pdbsum/4uob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4uob ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RVU4_DEIRA Q9RVU4_DEIRA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deira]]
+[[Category: Deinococcus radiodurans R1]]
 [[Category: Large Structures]]
-[[Category: Hall, D]]
+[[Category: Hall D]]
-[[Category: Klar, T]]
+[[Category: Klar T]]
-[[Category: McSweeney, S]]
+[[Category: McSweeney S]]
-[[Category: Moe, E]]
+[[Category: Moe E]]
-[[Category: Okvist, M]]
+[[Category: Okvist M]]
-[[Category: Sarre, A]]
+[[Category: Sarre A]]
-[[Category: Smalas, A O]]
+[[Category: Smalas AO]]
-[[Category: Timmins, J]]
+[[Category: Timmins J]]
-[[Category: Base excision repair]]
-[[Category: Deinococcus radioduran]]
-[[Category: Dna glycosylase]]
-[[Category: Endonuclease iii]]
-[[Category: Fes cluster]]
-[[Category: Lyase]]

4uob

From Proteopedia

Revision as of 07:29, 29 March 2023

Crystal structure of Deinococcus radiodurans Endonuclease III-3

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox