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.


3gpl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
==Crystal structure of the ternary complex of RecD2 with DNA and ADPNP==
==Crystal structure of the ternary complex of RecD2 with DNA and ADPNP==
-
<StructureSection load='3gpl' size='340' side='right' caption='[[3gpl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+
<StructureSection load='3gpl' size='340' side='right'caption='[[3gpl]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3gpl]] is a 4 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=3GPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPL FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3gpl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPL FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gp8|3gp8]], [[3e1s|3e1s]]</td></tr>
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gp8|3gp8]], [[3e1s|3e1s]]</div></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
+
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1902, recD2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [http://pdbe.org/3gpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [http://www.ebi.ac.uk/pdbsum/3gpl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpl 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=3gpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpl OCA], [https://pdbe.org/3gpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpl RCSB], [https://www.ebi.ac.uk/pdbsum/3gpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpl ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/RECDL_DEIRA RECDL_DEIRA]] DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.<ref>PMID:15466873</ref> <ref>PMID:19490894</ref>
+
[[https://www.uniprot.org/uniprot/RECDL_DEIRA RECDL_DEIRA]] DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.<ref>PMID:15466873</ref> <ref>PMID:19490894</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 32: Line 32:
==See Also==
==See Also==
-
*[[Exonuclease|Exonuclease]]
+
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 38: Line 38:
</StructureSection>
</StructureSection>
[[Category: Deira]]
[[Category: Deira]]
 +
[[Category: Large Structures]]
[[Category: Cook, N]]
[[Category: Cook, N]]
[[Category: Saikrishnan, K]]
[[Category: Saikrishnan, K]]

Revision as of 07:51, 16 March 2022

Crystal structure of the ternary complex of RecD2 with DNA and ADPNP

PDB ID 3gpl

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/3gpl"
Personal tools