This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1q3f

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:42, 9 December 2020

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Structural highlights

1q3f is a 3 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	1emh, 1ssp
Gene:	UNG OR DGU OR UNG15 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[UNG_HUMAN] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:608106]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.^[1] ^[2]

Function

[UNG_HUMAN] 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.

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

The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.

Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.,Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT Biochemistry. 2003 Nov 4;42(43):12455-60. PMID:14580190^[3]

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

References

↑ Imai K, Slupphaug G, Lee WI, Revy P, Nonoyama S, Catalan N, Yel L, Forveille M, Kavli B, Krokan HE, Ochs HD, Fischer A, Durandy A. Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nat Immunol. 2003 Oct;4(10):1023-8. Epub 2003 Sep 7. PMID:12958596 doi:http://dx.doi.org/10.1038/ni974
↑ Kavli B, Andersen S, Otterlei M, Liabakk NB, Imai K, Fischer A, Durandy A, Krokan HE, Slupphaug G. B cells from hyper-IgM patients carrying UNG mutations lack ability to remove uracil from ssDNA and have elevated genomic uracil. J Exp Med. 2005 Jun 20;201(12):2011-21. PMID:15967827 doi:10.1084/jem.20050042
↑ Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT. Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase. Biochemistry. 2003 Nov 4;42(43):12455-60. PMID:14580190 doi:10.1021/bi035372+

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1q3f"

@@ Line 1: / Line 1: @@
 ==Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA==
-<StructureSection load='1q3f' size='340' side='right' caption='[[1q3f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1q3f' size='340' side='right'caption='[[1q3f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q3f]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NRI:PHOSPHORIC+ACID+MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)+ESTER'>NRI</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1emh|1emh]], [[1ssp|1ssp]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1emh|1emh]], [[1ssp|1ssp]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UNG OR DGU OR UNG15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1q3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3f OCA], [http://pdbe.org/1q3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q3f RCSB], [http://www.ebi.ac.uk/pdbsum/1q3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3f ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1q3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3f OCA], [http://pdbe.org/1q3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q3f RCSB], [http://www.ebi.ac.uk/pdbsum/1q3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3f ProSAT]</span></td></tr>
 </table>
 == Disease ==
@@ Line 35: / Line 35: @@
 ==See Also==
-*[[DNA glycosylase|DNA glycosylase]]
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 == References ==
 <references/>
@@ Line 41: / Line 41: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Amzel, L M]]
 [[Category: Bianchet, M A]]

1q3f

From Proteopedia

Revision as of 07:42, 9 December 2020

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox