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.


3tfr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:26, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3tfr' size='340' side='right'caption='[[3tfr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3tfr' size='340' side='right'caption='[[3tfr]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3tfr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TFR FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3tfr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TFR 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=F3A:2-DEOXY-5-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]ADENOSINE'>F3A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2&#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;'>[[3tfs|3tfs]]</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=F3A:2-DEOXY-5-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]ADENOSINE'>F3A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3tfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfr OCA], [https://pdbe.org/3tfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tfr RCSB], [https://www.ebi.ac.uk/pdbsum/3tfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tfr 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=3tfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfr OCA], [https://pdbe.org/3tfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tfr RCSB], [https://www.ebi.ac.uk/pdbsum/3tfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tfr ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
+
[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The influence of water: Crystallization of (R/S)-alpha,beta-CHF-dATP with the preorganized pol beta-DNA complex shows that (S)-alpha,beta-CHF-dATP is preferentially bound to the active site with the CF fluorine proximal to a structural water bound to Asp276.
+
-
Stereospecific Formation of a Ternary Complex of (S)-alpha,beta-Fluoromethylene-dATP with DNA Pol beta.,Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Chembiochem. 2012 Mar 5;13(4):528-30. doi: 10.1002/cbic.201100738. Epub 2012 Feb , 7. PMID:22315190<ref>PMID:22315190</ref>
+
==See Also==
-
 
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3tfr" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Batra, V K]]
+
[[Category: Batra VK]]
-
[[Category: Beard, W A]]
+
[[Category: Beard WA]]
-
[[Category: Chamberlain, B T]]
+
[[Category: Chamberlain BT]]
-
[[Category: Goodman, M F]]
+
[[Category: Goodman MF]]
-
[[Category: Kadina, A P]]
+
[[Category: Kadina AP]]
-
[[Category: Kashemirov, B A]]
+
[[Category: Kashemirov BA]]
-
[[Category: McKenna, C E]]
+
[[Category: McKenna CE]]
-
[[Category: Shock, D D]]
+
[[Category: Shock DD]]
-
[[Category: Wilson, S H]]
+
[[Category: Wilson SH]]
-
[[Category: Dna polymerase]]
+
-
[[Category: Stereoselectivity]]
+
-
[[Category: Transferase-dna complex]]
+

Current revision

Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site

PDB ID 3tfr

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/3tfr"
Personal tools