6pbd: Difference between revisions

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<StructureSection load='6pbd' size='340' side='right'caption='[[6pbd]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
<StructureSection load='6pbd' size='340' side='right'caption='[[6pbd]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6pbd]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PBD FirstGlance]. <br>
<table><tr><td colspan='2'>[[6pbd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PBD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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]] 2.343&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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=6pbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbd OCA], [http://pdbe.org/6pbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pbd RCSB], [http://www.ebi.ac.uk/pdbsum/6pbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbd 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=6pbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pbd OCA], [https://pdbe.org/6pbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pbd RCSB], [https://www.ebi.ac.uk/pdbsum/6pbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pbd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/MTC1_CAUVC MTC1_CAUVC]] This methylase recognizes the double-stranded sequence GANTC and causes specific methylation on A-2 on both strands. Ccrm-mediated methylation has important cellular functions. Appears to contribute to the accurate cell-cycle control of DNA replication and cellular morphology.  
[https://www.uniprot.org/uniprot/CCRM_CAUVC CCRM_CAUVC] A beta subtype methylase that recognizes the double-stranded sequence 5'-GANTC-3' and methylates non-modifed A-2 on the hemimethylated, post-replicative DNA (Probable) (PubMed:12654995) (By similarity). Opens a bubble in the DNA at the recognition site, allowing precise recognition of the sequence and ensuring enzyme specificity (PubMed:31601797). Functions only in the predivisional cell. Responsible for 5'-GANTC-3' methylation in the cell; methylation of hemimethylated sites generated after replication fork passage occurs late in the predivisional cell, near completion of chromosome replication but prior to cell division. Contributes to the accurate cell-cycle control of DNA replication and cellular morphology (By similarity).[UniProtKB:B8GZ33]<ref>PMID:31601797</ref> <ref>PMID:12654995</ref> <ref>PMID:31601797</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Caulobacter vibrioides]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cheng, X]]
[[Category: Synthetic construct]]
[[Category: Horton, J R]]
[[Category: Cheng X]]
[[Category: Woodcock, C B]]
[[Category: Horton JR]]
[[Category: Base flipping]]
[[Category: Woodcock CB]]
[[Category: Dna methylation]]
[[Category: Gantc recognition]]
[[Category: Transferase-dna complex]]

Latest revision as of 10:26, 11 October 2023

DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATCDNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATC

Structural highlights

6pbd is a 4 chain structure with sequence from Caulobacter vibrioides and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.343Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCRM_CAUVC A beta subtype methylase that recognizes the double-stranded sequence 5'-GANTC-3' and methylates non-modifed A-2 on the hemimethylated, post-replicative DNA (Probable) (PubMed:12654995) (By similarity). Opens a bubble in the DNA at the recognition site, allowing precise recognition of the sequence and ensuring enzyme specificity (PubMed:31601797). Functions only in the predivisional cell. Responsible for 5'-GANTC-3' methylation in the cell; methylation of hemimethylated sites generated after replication fork passage occurs late in the predivisional cell, near completion of chromosome replication but prior to cell division. Contributes to the accurate cell-cycle control of DNA replication and cellular morphology (By similarity).[UniProtKB:B8GZ33][1] [2] [3]

Publication Abstract from PubMed

The Caulobacter crescentus cell cycle-regulated DNA methyltransferase (CcrM) methylates the adenine of hemimethylated GANTC after replication. Here we present the structure of CcrM in complex with double-stranded DNA containing the recognition sequence. CcrM contains an N-terminal methyltransferase domain and a C-terminal nonspecific DNA-binding domain. CcrM is a dimer, with each monomer contacting primarily one DNA strand: the methyltransferase domain of one molecule binds the target strand, recognizes the target sequence, and catalyzes methyl transfer, while the C-terminal domain of the second molecule binds the non-target strand. The DNA contacts at the 5-base pair recognition site results in dramatic DNA distortions including bending, unwinding and base flipping. The two DNA strands are pulled apart, creating a bubble comprising four recognized base pairs. The five bases of the target strand are recognized meticulously by stacking contacts, van der Waals interactions and specific Watson-Crick polar hydrogen bonds to ensure high enzymatic specificity.

The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.,Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X Nat Commun. 2019 Oct 10;10(1):4600. doi: 10.1038/s41467-019-12498-7. PMID:31601797[4]

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

References

  1. ↑ Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X. The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun. 2019 Oct 10;10(1):4600. doi: 10.1038/s41467-019-12498-7. PMID:31601797 doi:http://dx.doi.org/10.1038/s41467-019-12498-7
  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
  3. ↑ Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X. The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun. 2019 Oct 10;10(1):4600. doi: 10.1038/s41467-019-12498-7. PMID:31601797 doi:http://dx.doi.org/10.1038/s41467-019-12498-7
  4. ↑ Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X. The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site. Nat Commun. 2019 Oct 10;10(1):4600. doi: 10.1038/s41467-019-12498-7. PMID:31601797 doi:http://dx.doi.org/10.1038/s41467-019-12498-7

6pbd, resolution 2.34Å

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