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| | ==Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI== | | ==Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI== |
| - | <StructureSection load='4lyl' size='340' side='right' caption='[[4lyl]], [[Resolution|resolution]] 1.93Å' scene=''> | + | <StructureSection load='4lyl' size='340' side='right'caption='[[4lyl]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lyl]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LYL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lyl]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_PBS2 Bacillus phage PBS2] and [https://en.wikipedia.org/wiki/Gadus_morhua Gadus morhua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LYL FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1okb|1okb]]</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]] 1.93Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4lyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyl OCA], [https://pdbe.org/4lyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lyl RCSB], [https://www.ebi.ac.uk/pdbsum/4lyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyl ProSAT]</span></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=4lyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyl OCA], [http://pdbe.org/4lyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lyl RCSB], [http://www.ebi.ac.uk/pdbsum/4lyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyl 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] [[http://www.uniprot.org/uniprot/UNGI_BPPB2 UNGI_BPPB2]] This protein binds specifically and reversibly to the host uracil-DNA glycosylase, preventing removal of uracil residues from PBS2 DNA by the host uracil-excision repair system. | + | [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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[DNA glycosylase|DNA glycosylase]] | + | *[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]] |
| - | *[[Uracil-DNA glycosylase|Uracil-DNA glycosylase]] | + | *[[Uracil glycosylase inhibitor|Uracil glycosylase inhibitor]] |
| - | *[[Uracil-DNA glycosylase inhibitor|Uracil-DNA glycosylase inhibitor]]
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Uridine nucleosidase]] | + | [[Category: Bacillus phage PBS2]] |
| - | [[Category: Assefa, N G]] | + | [[Category: Gadus morhua]] |
| - | [[Category: Johnson, K A]] | + | [[Category: Large Structures]] |
| - | [[Category: Leiros, H K.S]] | + | [[Category: Assefa NG]] |
| - | [[Category: Moe, E]] | + | [[Category: Johnson KA]] |
| - | [[Category: Niiranen, L M.K]] | + | [[Category: Leiros H-KS]] |
| - | [[Category: Smalas, A O]] | + | [[Category: Moe E]] |
| - | [[Category: Willassen, N P]] | + | [[Category: Niiranen LMK]] |
| - | [[Category: Alpha/beta fold]] | + | [[Category: Smalas AO]] |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]] | + | [[Category: Willassen NP]] |
| - | [[Category: Hydrolysis]]
| + | |
| - | [[Category: Intracellular]]
| + | |
| 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]
Publication Abstract from PubMed
Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme-substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG-Ugi was determined to a resolution of 1.9 A with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG-Ugi complex with previously determined structures of UNG-Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (Kb) which is one order of magnitude larger than that for hUNG-Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein-Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi).,Assefa NG, Niiranen L, Johnson KA, Leiros HK, Smalas AO, Willassen NP, Moe E Acta Crystallogr D Biol Crystallogr. 2014 Aug 1;70(Pt 8):2093-100. doi:, 10.1107/S1399004714011699. Epub 2014 Jul 25. PMID:25084329[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Assefa NG, Niiranen L, Johnson KA, Leiros HK, Smalas AO, Willassen NP, Moe E. Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi). Acta Crystallogr D Biol Crystallogr. 2014 Aug 1;70(Pt 8):2093-100. doi:, 10.1107/S1399004714011699. Epub 2014 Jul 25. PMID:25084329 doi:http://dx.doi.org/10.1107/S1399004714011699
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