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1ydx

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Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

Structural highlights

1ydx is a 1 chain structure with sequence from Mycoplasma genitalium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T1SX_MYCGE The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. Subunit S dictates DNA sequences specificity (By similarity).

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 crystal structure of the eubacteria Mycoplasma genitalium ORF MG438 polypeptide, determined by multiple anomalous dispersion and refined at 2.3 A resolution, reveals the organization of S subunits from the Type I restriction and modification system. The structure consists of two globular domains, with about 150 residues each, separated by a pair of 40 residue long antiparallel alpha-helices. The globular domains correspond to the variable target recognition domains (TRDs), as previously defined for S subunits on sequence analysis, while the two helices correspond to the central (CR1) and C-terminal (CR2) conserved regions, respectively. The structure of the MG438 subunit presents an overall cyclic topology with an intramolecular 2-fold axis that superimposes the N and the C-half parts, each half containing a globular domain and a conserved helix. TRDs are found to be structurally related with the small domain of the Type II N6-adenine DNA MTase TaqI. These relationships together with the structural peculiarities of MG438, in particular the presence of the intramolecular quasi-symmetry, allow the proposal of a model for S subunits recognition of their DNA targets in agreement with previous experimental results. In the crystal, two subunits of MG438 related by a crystallographic 2-fold axis present a large contact area mainly involving the symmetric interactions of a cluster of exposed hydrophobic residues. Comparison with the recently reported structure of an S subunit from the archaea Methanococcus jannaschii highlights the structural features preserved despite a sequence identity below 20%, but also reveals important differences in the globular domains and in their disposition with respect to the conserved regions.

Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium.,Calisto BM, Pich OQ, Pinol J, Fita I, Querol E, Carpena X J Mol Biol. 2005 Aug 26;351(4):749-62. PMID:16038930^[1]

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

References

↑ Calisto BM, Pich OQ, Pinol J, Fita I, Querol E, Carpena X. Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium. J Mol Biol. 2005 Aug 26;351(4):749-62. PMID:16038930 doi:10.1016/j.jmb.2005.06.050

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='1ydx' size='340' side='right'caption='[[1ydx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ydx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33530 Atcc 33530]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YDX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ydx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_genitalium Mycoplasma genitalium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YDX 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></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]] 2.3&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MSE:SELENOMETHIONINE'>MSE</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=1ydx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ydx OCA], [http://pdbe.org/1ydx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ydx RCSB], [http://www.ebi.ac.uk/pdbsum/1ydx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ydx 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=1ydx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ydx OCA], [https://pdbe.org/1ydx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ydx RCSB], [https://www.ebi.ac.uk/pdbsum/1ydx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ydx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/T1SX_MYCGE T1SX_MYCGE]] The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. Subunit S dictates DNA sequences specificity (By similarity).
+[https://www.uniprot.org/uniprot/T1SX_MYCGE T1SX_MYCGE] The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. Subunit S dictates DNA sequences specificity (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33530]]
 [[Category: Large Structures]]
-[[Category: Carpena, X]]
+[[Category: Mycoplasma genitalium]]
-[[Category: Fita, I]]
+[[Category: Carpena X]]
-[[Category: Machado, B]]
+[[Category: Fita I]]
-[[Category: Pinol, J]]
+[[Category: Machado B]]
-[[Category: Querol, E]]
+[[Category: Pinol J]]
-[[Category: Quijada, O]]
+[[Category: Querol E]]
-[[Category: Dna binding protein]]
+[[Category: Quijada O]]
-[[Category: Type-i hsd]]

1ydx

From Proteopedia

Current revision

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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