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.


1dpi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1dpi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dpi, resolution 2.8&Aring;" /> '''STRUCTURE OF LARGE FR...)
Current revision (06:57, 7 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dpi.gif|left|200px]]<br /><applet load="1dpi" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dpi, resolution 2.8&Aring;" />
 
-
'''STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP'''<br />
 
-
==Overview==
+
==STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP==
-
The 3.3-A resolution crystal structure of the large proteolytic fragment, of Escherichia coli DNA polymerase I complexed with deoxythymidine, monophosphate consists of two domains, the smaller of which binds, zinc-deoxythymidine monophosphate. The most striking feature of the larger, domain is a deep crevice of the appropriate size and shape for binding, double-stranded B-DNA. A flexible subdomain may allow the enzyme to, surround completely the DNA substrate, thereby allowing processive, nucleotide polymerization without enzyme dissociation.
+
<StructureSection load='1dpi' size='340' side='right'caption='[[1dpi]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1dpi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DPI FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1dpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dpi OCA], [https://pdbe.org/1dpi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dpi RCSB], [https://www.ebi.ac.uk/pdbsum/1dpi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dpi ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPO1_ECOLI DPO1_ECOLI] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.
 +
== 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/dp/1dpi_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/main_output.php?pdb_ID=1dpi ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1DPI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DPI OCA].
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP., Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA, Nature. 1985 Feb 28-Mar 6;313(6005):762-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3883192 3883192]
+
-
[[Category: DNA-directed DNA polymerase]]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Beese, L.]]
+
[[Category: Beese L]]
-
[[Category: Ollis, D.]]
+
[[Category: Ollis D]]
-
[[Category: Steitz, T.]]
+
[[Category: Steitz T]]
-
[[Category: ZN]]
+
-
[[Category: nucleotidyltransferase]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:28:29 2007''
+

Current revision

STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP

PDB ID 1dpi

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/1dpi"
Personal tools