1dnp: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1dnp.jpg|left|200px]]


<!--
==STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE==
The line below this paragraph, containing "STRUCTURE_1dnp", creates the "Structure Box" on the page.
<StructureSection load='1dnp' size='340' side='right'caption='[[1dnp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dnp]] is a 2 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=1DNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNP FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MHF:5,10-METHENYL-6,7,8-TRIHYDROFOLIC+ACID'>MHF</scene></td></tr>
{{STRUCTURE_1dnp|  PDB=1dnp  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnp OCA], [https://pdbe.org/1dnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnp RCSB], [https://www.ebi.ac.uk/pdbsum/1dnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnp ProSAT]</span></td></tr>
 
</table>
'''STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE'''
== Function ==
 
[https://www.uniprot.org/uniprot/PHR_ECOLI PHR_ECOLI] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation.
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr &lt;&gt; Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr &lt;&gt; Pyr dinucleotide, suggesting that the Pyr &lt;&gt; Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr &lt;&gt; Pyr occurs over van der Waals contact distance.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dn/1dnp_consurf.spt"</scriptWhenChecked>
1DNP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNP OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Crystal structure of DNA photolyase from Escherichia coli., Park HW, Kim ST, Sancar A, Deisenhofer J, Science. 1995 Jun 30;268(5219):1866-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7604260 7604260]
</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=1dnp ConSurf].
[[Category: Deoxyribodipyrimidine photo-lyase]]
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Deisenhofer, J.]]
[[Category: Deisenhofer J]]
[[Category: Park, H W.]]
[[Category: Park H-W]]
[[Category: Sancar, A.]]
[[Category: Sancar A]]
[[Category: Carbon-carbon]]
[[Category: Dna repair]]
[[Category: Electron transfer]]
[[Category: Excitation energy transfer]]
[[Category: Lyase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:03:31 2008''

Latest revision as of 06:56, 7 February 2024

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE

1dnp, resolution 2.30Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=1dnp&oldid=4042128"