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6m9m

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Streptococcus mutans AlkD2 bound to inosine-5'-monophosphate

Structural highlights

6m9m is a 1 chain structure with sequence from Streptococcus mutans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.401Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0M3KL00_STRMG

Publication Abstract from PubMed

DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on alpha-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.

Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.,Shi R, Shen XX, Rokas A, Eichman BF Bioessays. 2018 Sep 28. doi: 10.1002/bies.201800133. PMID:30264543^[1]

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

References

↑ Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays. 2018 Sep 28. doi: 10.1002/bies.201800133. PMID:30264543 doi:http://dx.doi.org/10.1002/bies.201800133

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6m9m"

Categories: Large Structures | Streptococcus mutans | Eichman BF | Shi R

@@ Line 3: / Line 3: @@
 <StructureSection load='6m9m' size='340' side='right'caption='[[6m9m]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6m9m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25175 Atcc 25175]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M9M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6m9m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M9M 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=IMP:INOSINIC+ACID'>IMP</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]] 1.401&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ALKD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 ATCC 25175])</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=IMP:INOSINIC+ACID'>IMP</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=6m9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9m OCA], [http://pdbe.org/6m9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m9m RCSB], [http://www.ebi.ac.uk/pdbsum/6m9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9m 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=6m9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m9m OCA], [https://pdbe.org/6m9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m9m RCSB], [https://www.ebi.ac.uk/pdbsum/6m9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m9m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0M3KL00_STRMG A0A0M3KL00_STRMG]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 25175]]
 [[Category: Large Structures]]
-[[Category: Eichman, B F]]
+[[Category: Streptococcus mutans]]
-[[Category: Shi, R]]
+[[Category: Eichman BF]]
-[[Category: Heat-like repeat]]
+[[Category: Shi R]]
-[[Category: Nucleotide binding]]
-[[Category: Unknown function]]

6m9m

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Current revision

Streptococcus mutans AlkD2 bound to inosine-5'-monophosphate

Structural highlights

Function

Publication Abstract from PubMed

References

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