4fhd: Difference between revisions

Revision as of 19:48, 19 October 2022

Spore photoproduct lyase complexed with dinucleoside spore photoproduct

Structural highlights

4fhd is a 1 chain structure with sequence from Geobacillus thermodenitrificans NG80-2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	0TT, EEM, POP, SF4, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A4IQU1_GEOTN

Publication Abstract from PubMed

Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe-4S](1+) cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe-4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a beta-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the alpha-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.

Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme.,Benjdia A, Heil K, Barends TR, Carell T, Schlichting I Nucleic Acids Res. 2012 Jul 2. PMID:22761404^[1]

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

References

↑ Benjdia A, Heil K, Barends TR, Carell T, Schlichting I. Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme. Nucleic Acids Res. 2012 Jul 2. PMID:22761404 doi:10.1093/nar/gks603

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OCA

[1] Benjdia A, Heil K, Barends TR, Carell T, Schlichting I. Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme. Nucleic Acids Res. 2012 Jul 2. PMID:22761404 doi:10.1093/nar/gks603

[1]

@@ Line 1: / Line 1: @@
 ==Spore photoproduct lyase complexed with dinucleoside spore photoproduct==
-<StructureSection load='4fhd' size='340' side='right' caption='[[4fhd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4fhd' size='340' side='right'caption='[[4fhd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geotn Geotn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FHD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FHD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TT:1-[(2R,4S,5R)-5-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-2-YL]-5-[[(5R)-1-[(2R,4S,5R)-5-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-2-YL]-5-METHYL-2,4-BIS(OXIDANYLIDENE)-1,3-DIAZINAN-5-YL]METHYL]PYRIMIDINE-2,4-DIONE'>0TT</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TT:1-[(2R,4S,5R)-5-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-2-YL]-5-[[(5R)-1-[(2R,4S,5R)-5-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-2-YL]-5-METHYL-2,4-BIS(OXIDANYLIDENE)-1,3-DIAZINAN-5-YL]METHYL]PYRIMIDINE-2,4-DIONE'>0TT</scene>, <scene name='pdbligand=EEM:[(3S)-3-AMINO-4-HYDROXY-4-OXO-BUTYL]-[[(2S,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL]-METHYL-SELANIUM'>EEM</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fhc|4fhc]], [[4fhe|4fhe]], [[4fhf|4fhf]], [[4fhg|4fhg]]</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=4fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhd OCA], [https://pdbe.org/4fhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fhd RCSB], [https://www.ebi.ac.uk/pdbsum/4fhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhd ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GTNG_2348 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=420246 GEOTN])</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=4fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fhd OCA], [http://pdbe.org/4fhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fhd RCSB], [http://www.ebi.ac.uk/pdbsum/4fhd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fhd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A4IQU1_GEOTN A4IQU1_GEOTN]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Geotn]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
-[[Category: Barends, T R.M]]
+[[Category: Large Structures]]
-[[Category: Benjdia, A]]
+[[Category: Barends TRM]]
-[[Category: Carell, T]]
+[[Category: Benjdia A]]
-[[Category: Heil, K]]
+[[Category: Carell T]]
-[[Category: Schlichting, I]]
+[[Category: Heil K]]
-[[Category: Damaged dna]]
+[[Category: Schlichting I]]
-[[Category: Dna repair]]
-[[Category: Lyase]]
-[[Category: Partial tim-barrel]]

4fhd: Difference between revisions

Revision as of 19:48, 19 October 2022

Spore photoproduct lyase complexed with dinucleoside spore photoproduct

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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