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1vel

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Revision as of 00:02, 28 December 2023

Mycobacterium smegmatis Dps tetragonal form

Structural highlights

1vel is a 6 chain structure with sequence from Mycolicibacterium smegmatis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.99Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1vel' size='340' side='right'caption='[[1vel]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vel]] is a 6 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=1VEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vel]] is a 6 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=1VEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.99&#8491;</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]], [[1veq|1veq]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1vel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vel OCA], [https://pdbe.org/1vel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vel RCSB], [https://www.ebi.ac.uk/pdbsum/1vel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vel ProSAT]</span></td></tr>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus smegmatis trevisan 1889]]
 [[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]]

1vel

From Proteopedia

Revision as of 00:02, 28 December 2023

Mycobacterium smegmatis Dps tetragonal form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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