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.

4rtr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTTTA )

Structural highlights

4rtr is a 3 chain structure with sequence from Escherichia coli str. K-12 substr. MDS42 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 2.393Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DMA_ECOLI Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication.

Publication Abstract from PubMed

DNA adenine methyltransferase (Dam) is widespread and conserved among the gamma-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.

Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.,Horton JR, Zhang X, Blumenthal RM, Cheng X Nucleic Acids Res. 2015 Apr 6. pii: gkv251. PMID:25845600^[1]

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

References

↑ Horton JR, Zhang X, Blumenthal RM, Cheng X. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic Acids Res. 2015 Apr 6. pii: gkv251. PMID:25845600 doi:http://dx.doi.org/10.1093/nar/gkv251

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rtr"

Categories: Escherichia coli str. K-12 substr. MDS42 | Large Structures | Synthetic construct | Cheng X | Horton JR

@@ Line 1: / Line 1: @@
 ==Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTTTA )==
-<StructureSection load='4rtr' size='340' side='right' caption='[[4rtr]], [[Resolution|resolution]] 2.39&Aring;' scene=''>
+<StructureSection load='4rtr' size='340' side='right'caption='[[4rtr]], [[Resolution|resolution]] 2.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rtr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RTR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rtr]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MDS42 Escherichia coli str. K-12 substr. MDS42] 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=4RTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RTR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.393&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2g1p|2g1p]], [[2ore|2ore]], [[4rtj|4rtj]], [[4rtk|4rtk]], [[4rtl|4rtl]], [[4rtm|4rtm]], [[4rtn|4rtn]], [[4rto|4rto]], [[4rtp|4rtp]], [[4rtq|4rtq]], [[4rts|4rts]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=4rtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtr OCA], [http://pdbe.org/4rtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rtr RCSB], [http://www.ebi.ac.uk/pdbsum/4rtr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtr 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=4rtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtr OCA], [https://pdbe.org/4rtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rtr RCSB], [https://www.ebi.ac.uk/pdbsum/4rtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DMA_ECOLI DMA_ECOLI] Methylates DNA within the sequence GATC and protects the DNA from cleavage by the restriction endonuclease MboI. Although it shares sequence specificity with a number of type II restriction endonucleases and methylases, it is thought to act in postreplication mismatch repair rather than as a part of a restriction modification system. May also play a role in DNA replication.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 22: @@
 ==See Also==
 *[[DNA adenine methylase|DNA adenine methylase]]
+*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cheng, X]]
+[[Category: Escherichia coli str. K-12 substr. MDS42]]
-[[Category: Horton, J R]]
+[[Category: Large Structures]]
-[[Category: Bacterial virulence]]
+[[Category: Synthetic construct]]
-[[Category: Base flipping]]
+[[Category: Cheng X]]
-[[Category: Dam methylation]]
+[[Category: Horton JR]]
-[[Category: Gatc recognition]]
-[[Category: Methylation-independent transcriptional repressor]]
-[[Category: Transferase-dna complex]]

4rtr

From Proteopedia

Current revision

Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTTTA )

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox