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2w9b

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Revision as of 09:37, 26 September 2018

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

Structural highlights

2w9b is a 6 chain structure with sequence from Sulso. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:	,
Related:	2asl, 1s0m, 2jeg, 1rys, 2v4s, 2j6t, 1n56, 2atl, 1jx4, 2c22, 2va2, 1s97, 2agq, 2ago, 2jej, 2w9c, 2asj, 2w9a, 2asd, 1jxl, 1n48, 2bq3, 2uvu, 2j6u, 2agp, 2c2r, 1s0n, 2w8l, 2jef, 1s0o, 2uvw, 2bqr, 2jei, 2bqu, 2au0, 1s9f, 2c28, 2v9w, 2v4r, 2c2e, 1ryr, 2c2d, 2uvv, 2v4q, 2j6s, 2br0, 1s10, 2uvr, 2va3, 2w8k, 2v4t
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Previous work has shown that Y-family DNA polymerases tolerate large DNA adducts, but a substantial decrease in catalytic efficiency and fidelity occurs during bypass of N(2),N(2)-dimethyl (Me(2))-substituted guanine (N(2),N(2)-Me(2)G), in contrast to a single methyl substitution. Therefore, it is unclear why the addition of two methyl groups is so disruptive. The presence of N(2),N(2)-Me(2)G lowered the catalytic efficiency of the model enzyme Sulfolobus solfataricus Dpo4 16,000-fold. Dpo4 inserted dNTPs almost at random during bypass of N(2),N(2)-Me(2)G, and much of the enzyme was kinetically trapped by an inactive ternary complex when N(2),N(2)-Me(2)G was present, as judged by a reduced burst amplitude (5% of total enzyme) and kinetic modeling. One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine (C(dd)) opposite template N(2),N(2)-Me(2)G in a post-insertion position showed C(dd) folded back into the minor groove, as a catalytically incompetent complex. A second crystal had two unique orientations for the primer terminal C(dd) as follows: (i) flipped into the minor groove and (ii) a long pairing with N(2),N(2)-Me(2)G in which one hydrogen bond exists between the O-2 atom of C(dd) and the N-1 atom of N(2),N(2)-Me(2)G, with a second water-mediated hydrogen bond between the N-3 atom of C(dd) and the O-6 atom of N(2),N(2)-Me(2)G. A crystal structure of Dpo4 with dTTP opposite template N(2),N(2)-Me(2)G revealed a wobble orientation. Collectively, these results explain, in a detailed manner, the basis for the reduced efficiency and fidelity of Dpo4-catalyzed bypass of N(2),N(2)-Me(2)G compared with mono-substituted N(2)-alkyl G adducts.

Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES.,Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP J Biol Chem. 2009 Jun 26;284(26):17687-99. PMID:19542237^[1]

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

References

↑ Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP. Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES. J Biol Chem. 2009 Jun 26;284(26):17687-99. PMID:19542237 doi:284/26/17687

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w9b"

@@ Line 1: / Line 1: @@
-==BINARY COMPLEX OF DPO4 BOUND TO N2,N2-DIMETHYL-DEOXYGUANOSINE MODIFIED DNA==
+==Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA==
 <StructureSection load='2w9b' size='340' side='right' caption='[[2w9b]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
 == Structural highlights ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w9b_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w9/2w9b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 45: / Line 45: @@
 [[Category: Zhang, H]]
 [[Category: Adduct]]
+[[Category: Cytoplasm]]
 [[Category: Dna]]
 [[Category: Dna damage]]

2w9b

From Proteopedia

Revision as of 09:37, 26 September 2018

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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