1bgx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1bgx" [edit=sysop:move=sysop])
Line 1: Line 1:
-
{{Seed}}
+
<table cellpadding='5'><tr><td style='background-color: yellow;border:2px solid black;font-size:150%;'>
-
{{Template:Possible_fraud}}
+
WARNING: This structure was flagged as problematic. For additional information see '''2009, December:''' at [[Retractions and Fraud]].</td></tr></table>
-
[[Image:1bgx.png|left|200px]]
+
==TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB==
 +
<StructureSection load='1bgx' size='340' side='right' caption='[[1bgx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1bgx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BGX FirstGlance]. <br>
 +
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
 +
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=1bgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bgx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bgx RCSB], [http://www.ebi.ac.uk/pdbsum/1bgx PDBsum]</span></td></tr>
 +
</table>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bg/1bgx_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We report the crystal structure of Thermus aquaticus DNA polymerase I in complex with an inhibitory Fab, TP7, directed against the native enzyme. Some of the residues present in a helical conformation in the native enzyme have adopted a gamma turn conformation in the complex. Taken together, structural information that describes alteration of helical structure and solution studies that demonstrate the ability of TP7 to inhibit 100% of the polymerase activity of the enzyme suggest that the change in conformation is probably caused by trapping of an intermediate in the helix-coil dynamics of this helix by the Fab. Antibodies directed against modified helices in proteins have long been anticipated. The present structure provides direct crystallographic evidence. The Fab binds within the DNA binding cleft of the polymerase domain, interacting with several residues that are used by the enzyme in binding the primer:template complex. This result unequivocally corroborates inferences drawn from binding experiments and modeling calculations that the inhibitory activity of this Fab is directly attributable to its interference with DNA binding by the polymerase domain of the enzyme. The combination of interactions made by the Fab residues in both the polymerase and the vestigial editing nuclease domain of the enzyme reveal the structural basis of its preference for binding to DNA polymerases of the Thermus species. The orientation of the structure-specific nuclease domain with respect to the polymerase domain is significantly different from that seen in other structures of this polymerase. This reorientation does not appear to be antibody-induced and implies remarkably high relative mobility between these two domains.
-
<!--
+
Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.,Murali R, Sharkey DJ, Daiss JL, Murthy HM Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12562-7. PMID:9770525<ref>PMID:9770525</ref>
-
The line below this paragraph, containing "STRUCTURE_1bgx", creates the "Structure Box" on the page.
+
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
-
or leave the SCENE parameter empty for the default display.
+
-
-->
+
-
{{STRUCTURE_1bgx| PDB=1bgx | SCENE= }}
+
-
===TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB===
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
-
 
+
==See Also==
-
<!--
+
*[[DNA polymerase|DNA polymerase]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_9770525}}, adds the Publication Abstract to the page
+
*[[Extremophiles|Extremophiles]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 9770525 is the PubMed ID number.
+
*[[Retractions and Fraud|Retractions and Fraud]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_9770525}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
1BGX is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BGX OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:9770525</ref><references group="xtra"/>
+
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
-
[[Category: Daiss, J L.]]
+
[[Category: Daiss, J L]]
-
[[Category: Murali, R.]]
+
[[Category: Murali, R]]
-
[[Category: Murthy, H M.Krishna.]]
+
[[Category: Murthy, H M.Krishna]]
-
[[Category: Sharkey, D J.]]
+
[[Category: Sharkey, D J]]
[[Category: Dna polymerase]]
[[Category: Dna polymerase]]
[[Category: Fab]]
[[Category: Fab]]
Line 38: Line 49:
[[Category: Inhibitor design]]
[[Category: Inhibitor design]]
[[Category: Pcr]]
[[Category: Pcr]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:47:44 2009''
 

Revision as of 08:29, 18 November 2014

WARNING: This structure was flagged as problematic. For additional information see 2009, December: at Retractions and Fraud.

TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB

1bgx, resolution 2.30Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA, Eric Martz

Retrieved from "http://proteopedia.org/wiki/index.php/1bgx"
Personal tools