2e0i

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor

Structural highlights

2e0i is a 4 chain structure with sequence from Sulfurisphaera tokodaii str. 7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

F9VNB1_SULTO

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

UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.,Fujihashi M, Numoto N, Kobayashi Y, Mizushima A, Tsujimura M, Nakamura A, Kawarabayasi Y, Miki K J Mol Biol. 2007 Jan 26;365(4):903-10. Epub 2006 Oct 7. PMID:17107688^[1]

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

References

↑ Fujihashi M, Numoto N, Kobayashi Y, Mizushima A, Tsujimura M, Nakamura A, Kawarabayasi Y, Miki K. Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor. J Mol Biol. 2007 Jan 26;365(4):903-10. Epub 2006 Oct 7. PMID:17107688 doi:10.1016/j.jmb.2006.10.012

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/2e0i"

@@ Line 3: / Line 3: @@
 <StructureSection load='2e0i' size='340' side='right'caption='[[2e0i]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2e0i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulto Sulto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E0I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2e0i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E0I FirstGlance]. <br>
-</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ST0889 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </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=2e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e0i OCA], [https://pdbe.org/2e0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e0i RCSB], [https://www.ebi.ac.uk/pdbsum/2e0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e0i ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/F9VNB1_SULTO F9VNB1_SULTO]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/2e0i_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Deoxyribodipyrimidine photo-lyase]]
 [[Category: Large Structures]]
-[[Category: Sulto]]
+[[Category: Sulfurisphaera tokodaii str. 7]]
-[[Category: Fujihashi, M]]
+[[Category: Fujihashi M]]
-[[Category: Kawarabayashi, Y]]
+[[Category: Kawarabayashi Y]]
-[[Category: Kobayashi, Y]]
+[[Category: Kobayashi Y]]
-[[Category: Miki, K]]
+[[Category: Miki K]]
-[[Category: Mizushima, A]]
+[[Category: Mizushima A]]
-[[Category: Nakamura, A]]
+[[Category: Nakamura A]]
-[[Category: Numoto, N]]
+[[Category: Numoto N]]
-[[Category: Tsujimura, M]]
+[[Category: Tsujimura M]]
-[[Category: Dna repair]]
-[[Category: Fad]]
-[[Category: Lyase]]
-[[Category: Photolyase]]
-[[Category: Sulfolobus tokodaii]]

2e0i

From Proteopedia

Current revision

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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