1nw7: Difference between revisions

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<StructureSection load='1nw7' size='340' side='right'caption='[[1nw7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='1nw7' size='340' side='right'caption='[[1nw7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nw7]] is a 1 chain structure with sequence from [http://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=1NW7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NW7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nw7]] 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=1NW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NW7 FirstGlance]. <br>
</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=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.1&#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;'>[[1eg2|1eg2]], [[1nw5|1nw5]], [[1nw6|1nw6]], [[1nw8|1nw8]]</div></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=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsrIM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</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=1nw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nw7 OCA], [https://pdbe.org/1nw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nw7 RCSB], [https://www.ebi.ac.uk/pdbsum/1nw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nw7 ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nw7 OCA], [http://pdbe.org/1nw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nw7 RCSB], [http://www.ebi.ac.uk/pdbsum/1nw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nw7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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=1nw7 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=1nw7 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structures of RsrI DNA methyltransferase (M.RsrI) bound to the substrate S-adenosyl-l-methionine (AdoMet), the product S-adenosyl-l-homocysteine (AdoHcy), the inhibitor sinefungin, as well as a mutant apo-enzyme have been determined by x-ray crystallography. Two distinct binding configurations were observed for the three ligands. The substrate AdoMet adopts a bent shape that directs the activated methyl group toward the active site near the catalytic DPPY motif. The product AdoHcy and the competitive inhibitor sinefungin bind with a straight conformation in which the amino acid moiety occupies a position near the activated methyl group in the AdoMet complex. Analysis of ligand binding in comparison with other DNA methyltransferases reveals a small, common subset of available conformations for the ligand. The structures of M.RsrI with the non-substrate ligands contained a bound chloride ion in the AdoMet carboxylate-binding pocket, explaining its inhibition by chloride salts. The L72P mutant of M.RsrI is the first DNA methyltransferase structure without bound ligand. With respect to the wild-type protein, it had a larger ligand-binding pocket and displayed movement of a loop (223-227) that is responsible for binding the ligand, which may account for the weaker affinity of the L72P mutant for AdoMet. These studies show the subtle changes in the tight specific interactions of substrate, product, and an inhibitor with M.RsrI and help explain how each displays its unique effect on the activity of the enzyme.
Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.,Thomas CB, Scavetta RD, Gumport RI, Churchill ME J Biol Chem. 2003 Jul 11;278(28):26094-101. Epub 2003 May 4. PMID:12732637<ref>PMID:12732637</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nw7" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__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: Scavetta, R D]]
[[Category: Scavetta RD]]
[[Category: Thomas, C B]]
[[Category: Thomas CB]]
[[Category: Adenine dna methyltransferase]]
[[Category: Rossmann fold]]
[[Category: S-adenosyl homocysteine]]
[[Category: Transferase]]

Latest revision as of 11:00, 14 February 2024

Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to S-ADENOSYL-L-HOMOCYSTEINEStructure of the beta class N6-adenine DNA methyltransferase RsrI bound to S-ADENOSYL-L-HOMOCYSTEINE

Structural highlights

1nw7 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 2.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

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

1nw7, resolution 2.10Å

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