1jms

From Proteopedia

(Difference between revisions)

Revision as of 09:06, 17 January 2018

Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase

Structural highlights

1jms is a 1 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1bpx, 1bpy, 1bpz, 1kan, 1kny
Gene:	TDT (LK3 transgenic mice)
Activity:	DNA nucleotidylexotransferase, with EC number 2.7.7.31
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TDT_MOUSE] Template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. One of the in vivo functions of this enzyme is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells.

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 crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.

Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.,Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C EMBO J. 2002 Feb 1;21(3):427-39. PMID:11823435^[1]

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

References

↑ Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C. Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase. EMBO J. 2002 Feb 1;21(3):427-39. PMID:11823435

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1jms"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase==
 <StructureSection load='1jms' size='340' side='right' caption='[[1jms]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TDT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_nucleotidylexotransferase DNA nucleotidylexotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.31 2.7.7.31] </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=1jms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jms OCA], [http://pdbe.org/1jms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jms RCSB], [http://www.ebi.ac.uk/pdbsum/1jms PDBsum]</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=1jms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jms OCA], [http://pdbe.org/1jms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jms RCSB], [http://www.ebi.ac.uk/pdbsum/1jms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jms ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jm/1jms_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jm/1jms_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 31: @@
 </div>
 <div class="pdbe-citations 1jms" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[DNA polymerase|DNA polymerase]]
 == References ==
 <references/>

1jms

From Proteopedia

Revision as of 09:06, 17 January 2018

Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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