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| | ==crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)== | | ==crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)== |
| - | <StructureSection load='1okb' size='340' side='right' caption='[[1okb]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='1okb' size='340' side='right'caption='[[1okb]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1okb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atlantic_cod Atlantic cod]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OKB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1okb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gadus_morhua Gadus morhua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OKB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=1okb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okb OCA], [http://pdbe.org/1okb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1okb RCSB], [http://www.ebi.ac.uk/pdbsum/1okb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1okb ProSAT]</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=1okb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okb OCA], [https://pdbe.org/1okb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1okb RCSB], [https://www.ebi.ac.uk/pdbsum/1okb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1okb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q9I983_GADMO Q9I983_GADMO]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).[RuleBase:RU003780][HAMAP-Rule:MF_03166] | + | [https://www.uniprot.org/uniprot/Q9I983_GADMO Q9I983_GADMO] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).[RuleBase:RU003780][HAMAP-Rule:MF_03166] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[DNA glycosylase|DNA glycosylase]] | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atlantic cod]] | + | [[Category: Gadus morhua]] |
| - | [[Category: Uridine nucleosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Lanes, O]] | + | [[Category: Lanes O]] |
| - | [[Category: Leiros, I]] | + | [[Category: Leiros I]] |
| - | [[Category: Moe, E]] | + | [[Category: Moe E]] |
| - | [[Category: Smalas, A O]] | + | [[Category: Smalas AO]] |
| - | [[Category: Willassen, N P]] | + | [[Category: Willassen NP]] |
| - | [[Category: Base excision repair]]
| + | |
| - | [[Category: Cold-adaptation]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Structure-function relationship]]
| + | |
| - | [[Category: Uracil-dna glycosylase]]
| + | |
| Structural highlights
Function
Q9I983_GADMO Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).[RuleBase:RU003780][HAMAP-Rule:MF_03166]
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
Uracil-DNA glycosylase (UDG; EC 3.2.2.3) is a DNA-repair protein that catalyses the hydrolysis of promutagenic uracil residues from single- or double-stranded DNA, generating free uracil and abasic DNA. The crystal structure of the catalytic domain of cod uracil-DNA glycosylase (cUDG) has been determined to 1.9 A resolution, with final R factors of 18.61 and 20.57% for the working and test sets of reflections, respectively. This is the first crystal structure of a uracil-DNA glycosylase from a cold-adapted species and a detailed comparison with the human enzyme is performed in order to rationalize the cold-adapted behaviour of the cod enzyme at the structural level. The catalytic domain of cUDG comprises 223 residues, with a sequence identity to the human UDG of 75%. The tertiary structures of the two enzymes are also similar, with an overall displacement in main-chain atomic positions of 0.63 A. The amino-acid substitutions and the differences in intramolecular hydrogen bonds, hydrophobic interactions, ion-pair interactions and electrostatic potentials are compared and discussed in order to gain insight into the factors that cause the increased activity and reduced thermostability of the cod enzyme. In particular, the reduced number of strong ion-pair interactions in the C-terminal half of cUDG is believed to greatly affect the flexibility and/or stability. Increased positive electrostatic surface potential on the DNA-facing side of cUDG seems to be responsible for increasing the affinity for the negatively charged DNA compared with that of hUDG.
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.,Leiros I, Moe E, Lanes O, Smalas AO, Willassen NP Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1357-65. Epub 2003, Jul 23. PMID:12876336[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Leiros I, Moe E, Lanes O, Smalas AO, Willassen NP. The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features. Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1357-65. Epub 2003, Jul 23. PMID:12876336
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