1eg2: Difference between revisions

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<StructureSection load='1eg2' size='340' side='right'caption='[[1eg2]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='1eg2' size='340' side='right'caption='[[1eg2]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1eg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EG2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1eg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EG2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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]] 1.75&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</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=1eg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg2 OCA], [https://pdbe.org/1eg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eg2 RCSB], [https://www.ebi.ac.uk/pdbsum/1eg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eg2 ProSAT], [https://www.topsan.org/Proteins/MCSG/1eg2 TOPSAN]</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=1eg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg2 OCA], [https://pdbe.org/1eg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eg2 RCSB], [https://www.ebi.ac.uk/pdbsum/1eg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eg2 ProSAT], [https://www.topsan.org/Proteins/MCSG/1eg2 TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/MTR1_RHOSH MTR1_RHOSH]] This methylase recognizes the double-stranded sequence GAATTC, causes specific methylation on A-? on both strands, and protects the DNA from cleavage by the RsrI endonuclease.  
[https://www.uniprot.org/uniprot/MTR1_CERSP MTR1_CERSP] A beta subtype methylase, recognizes the double-stranded sequence 5'-GAATTC-3', methylates A-3 on both strands, and protects the DNA from cleavage by the RsrI endonuclease.<ref>PMID:2690017</ref> <ref>PMID:12654995</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1eg2 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1eg2 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA methylation is important in cellular, developmental and disease processes, as well as in bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine and adenine is a common mode of protection against restriction endonucleases afforded by the bacterial methyltransferases. The first structure of an N:6-adenine methyltransferase belonging to the beta class of bacterial methyltransferases is described here. The structure of M. RSR:I from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other methyltransferases, the enzyme contains the methylase fold and has well-defined substrate binding pockets. The catalytic core most closely resembles the PVU:II methyltransferase, a cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket observed in M. RSR:I is expected because it methylates adenine. However, the most striking difference between the RSR:I methyltransferase and the other bacterial enzymes is the structure of the putative DNA target recognition domain, which is formed in part by two helices on an extended arm of the protein on the face of the enzyme opposite the active site. This observation suggests that a dramatic conformational change or oligomerization may take place during DNA binding and methylation.
Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.,Scavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME Nucleic Acids Res. 2000 Oct 15;28(20):3950-61. PMID:11024175<ref>PMID:11024175</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1eg2" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Rhodococcus capsulatus molisch 1907]]
[[Category: Cereibacter sphaeroides]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Churchill, M E.A]]
[[Category: Churchill MEA]]
[[Category: Gumport, R I]]
[[Category: Gumport RI]]
[[Category: Joachimiak, A]]
[[Category: Joachimiak A]]
[[Category: Structural genomic]]
[[Category: Scavetta RD]]
[[Category: Scavetta, R D]]
[[Category: Szegedi S]]
[[Category: Szegedi, S]]
[[Category: Thomas CB]]
[[Category: Thomas, C B]]
[[Category: Walsh MA]]
[[Category: Walsh, M A]]
[[Category: Dna binding]]
[[Category: Dna methylation]]
[[Category: Dna modification]]
[[Category: Exocyclic amino dna methyltransferase rsri]]
[[Category: Mcsg]]
[[Category: PSI, Protein structure initiative]]
[[Category: Rossmann fold]]
[[Category: Transferase]]

Latest revision as of 10:02, 7 February 2024

CRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 ADENOSINE) METHYLTRANSFERASE (M.RSRI)CRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 ADENOSINE) METHYLTRANSFERASE (M.RSRI)

Structural highlights

1eg2 is a 1 chain structure with sequence from Cereibacter sphaeroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.75Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

MTR1_CERSP A beta subtype methylase, recognizes the double-stranded sequence 5'-GAATTC-3', methylates A-3 on both strands, and protects the DNA from cleavage by the RsrI endonuclease.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Kaszubska W, Aiken C, O'Connor CD, Gumport RI. Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences. Nucleic Acids Res. 1989 Dec 25;17(24):10403-25. PMID:2690017 doi:10.1093/nar/17.24.10403
  2. ↑ Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 2003 Apr 1;31(7):1805-12. PMID:12654995

1eg2, resolution 1.75Å

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