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| | <StructureSection load='1veq' size='340' side='right'caption='[[1veq]], [[Resolution|resolution]] 3.98Å' scene=''> | | <StructureSection load='1veq' size='340' side='right'caption='[[1veq]], [[Resolution|resolution]] 3.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1veq]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1veq]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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]] 3.98Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vei|1vei]], [[1vel|1vel]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></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=1veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1veq OCA], [https://pdbe.org/1veq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1veq RCSB], [https://www.ebi.ac.uk/pdbsum/1veq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1veq 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=1veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1veq OCA], [https://pdbe.org/1veq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1veq RCSB], [https://www.ebi.ac.uk/pdbsum/1veq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1veq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DPS_MYCS2 DPS_MYCS2]] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage (By similarity).
| + | [https://www.uniprot.org/uniprot/DPS_MYCSM DPS_MYCSM] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage.<ref>PMID:12466274</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus smegmatis trevisan 1889]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chatterji, D]] | + | [[Category: Mycolicibacterium smegmatis]] |
| - | [[Category: Das, S]] | + | [[Category: Chatterji D]] |
| - | [[Category: Gupta, S]] | + | [[Category: Das S]] |
| - | [[Category: Roy, S]] | + | [[Category: Gupta S]] |
| - | [[Category: Sekar, K]] | + | [[Category: Roy S]] |
| - | [[Category: Vijayan, M]] | + | [[Category: Sekar K]] |
| - | [[Category: Dna binding protein]]
| + | [[Category: Vijayan M]] |
| - | [[Category: Dna-binding protein]]
| + | |
| Structural highlights
Function
DPS_MYCSM Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage.[1]
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 structure of the DNA binding protein from starved cells from Mycobacterium smegmatis has been determined in three crystal forms and has been compared with those of similar proteins from other sources. The dodecameric molecule can be described as a distorted icosahedron. The interfaces among subunits are such that the dodecameric molecule appears to have been made up of stable trimers. The situation is similar in the proteins from Escherichia coli and Agrobacterium tumefaciens, which are closer to the M.smegmatis protein in sequence and structure than those from other sources, which appear to form a dimer first. Trimerisation is aided in the three proteins by the additional N-terminal stretches that they possess. The M.smegmatis protein has an additional C-terminal stretch compared to other related proteins. The stretch, known to be involved in DNA binding, is situated on the surface of the molecule. A comparison of the available structures permits a delineation of the rigid and flexible regions in the molecule. The subunit interfaces around the molecular dyads, where the ferroxidation centres are located, are relatively rigid. Regions in the vicinity of the acidic holes centred around molecular 3-fold axes, are relatively flexible. So are the DNA binding regions. The crystal structures of the protein from M.smegmatis confirm that DNA molecules can occupy spaces within the crystal without disturbing the arrangement of the protein molecules. However, contrary to earlier suggestions, the spaces do not need to be between layers of protein molecules. The cubic form provides an arrangement in which grooves, which could hold DNA molecules, criss-cross the crystal.
X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules.,Roy S, Gupta S, Das S, Sekar K, Chatterji D, Vijayan M J Mol Biol. 2004 Jun 18;339(5):1103-13. PMID:15178251[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gupta S, Chatterji D. Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein from stationary phase cells. J Biol Chem. 2003 Feb 14;278(7):5235-41. Epub 2002 Dec 3. PMID:12466274 doi:http://dx.doi.org/10.1074/jbc.M208825200
- ↑ Roy S, Gupta S, Das S, Sekar K, Chatterji D, Vijayan M. X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules. J Mol Biol. 2004 Jun 18;339(5):1103-13. PMID:15178251 doi:10.1016/j.jmb.2004.04.042
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