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.
1q0t
From Proteopedia
(Difference between revisions)
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
==Ternary Structure of T4DAM with AdoHcy and DNA== | ==Ternary Structure of T4DAM with AdoHcy and DNA== | ||
| - | <StructureSection load='1q0t' size='340' side='right' caption='[[1q0t]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='1q0t' size='340' side='right'caption='[[1q0t]], [[Resolution|resolution]] 3.10Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1q0t]] is a 4 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1q0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0T FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> | |
| - | <tr id=' | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0t OCA], [https://pdbe.org/1q0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0t RCSB], [https://www.ebi.ac.uk/pdbsum/1q0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0t ProSAT]</span></td></tr> |
| - | + | ||
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/DMA_BPT4 DMA_BPT4] This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands. |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 22: | Line 20: | ||
</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=1q0t 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=1q0t ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | DNA-adenine methylation at certain GATC sites plays a pivotal role in bacterial and phage gene expression as well as bacterial virulence. We report here the crystal structures of the bacteriophage T4Dam DNA adenine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-L-homocysteine (AdoHcy) and in a ternary complex with a synthetic 12-bp DNA duplex and AdoHcy. T4Dam contains two domains: a seven-stranded catalytic domain that harbors the binding site for AdoHcy and a DNA binding domain consisting of a five-helix bundle and a beta-hairpin that is conserved in the family of GATC-related MTase orthologs. Unexpectedly, the sequence-specific T4Dam bound to DNA in a nonspecific mode that contained two Dam monomers per synthetic duplex, even though the DNA contains a single GATC site. The ternary structure provides a rare snapshot of an enzyme poised for linear diffusion along the DNA. | ||
| - | + | ==See Also== | |
| - | + | *[[DNA adenine methylase|DNA adenine methylase]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Escherichia virus T4]] |
| - | [[Category: Cheng | + | [[Category: Large Structures]] |
| - | [[Category: Dong | + | [[Category: Cheng X]] |
| - | [[Category: Hattman | + | [[Category: Dong A]] |
| - | [[Category: Horton | + | [[Category: Hattman S]] |
| - | [[Category: Kossykh | + | [[Category: Horton JR]] |
| - | [[Category: Schlagman | + | [[Category: Kossykh V]] |
| - | [[Category: Yang | + | [[Category: Schlagman SL]] |
| - | [[Category: Zhang | + | [[Category: Yang Z]] |
| - | [[Category: Zhang | + | [[Category: Zhang X]] |
| - | [[Category: Zhou | + | [[Category: Zhang XJ]] |
| - | + | [[Category: Zhou L]] | |
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Ternary Structure of T4DAM with AdoHcy and DNA
| |||||||||||
Categories: Escherichia virus T4 | Large Structures | Cheng X | Dong A | Hattman S | Horton JR | Kossykh V | Schlagman SL | Yang Z | Zhang X | Zhang XJ | Zhou L
