This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1ydx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:23, 25 April 2018

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

Structural highlights

1ydx is a 1 chain structure with sequence from Atcc 33530. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
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 1: / Line 1: @@
 ==Crystal structure of Type-I restriction-modification system S subunit from M. genitalium==
 <StructureSection load='1ydx' size='340' side='right' caption='[[1ydx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </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>
 <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='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]</span></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>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1ydx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1ydx_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1ydx

From Proteopedia

Revision as of 06:23, 25 April 2018

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

Personal tools

Navigation

Search

Toolbox