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2dpm

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Revision as of 11:34, 10 February 2021

DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE

Structural highlights

2dpm is a 1 chain structure with sequence from "diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	DPNM ("Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886)
Activity:	Site-specific DNA-methyltransferase (adenine-specific), with EC number 2.1.1.72
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MTD21_STREE] This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands, and protects the DNA from cleavage by the DpnII endonuclease.

Evolutionary Conservation

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

Publication Abstract from PubMed

BACKGROUND:. Methyltransferases (Mtases) catalyze the transfer of methyl groups from S-adenosylmethionine (AdoMet) to a variety of small molecular and macromolecular substrates. These enzymes contain a characteristic alpha/beta structural fold. Four groups of DNA Mtases have been defined and representative structures have been determined for three groups. DpnM is a DNA Mtase that acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for which no structures are known. RESULTS:. The structure of DpnM in complex with AdoMet was determined at 1.80 A resolution. The protein comprises a consensus Mtase fold with a helical cluster insert. DpnM binds AdoMet in a similar manner to most other Mtases and the enzyme contains a hollow that can accommodate DNA. The helical cluster supports a shelf within the hollow that may recognize the target sequence. Modeling studies indicate a potential site for binding the target adenine, everted from the DNA helix. Comparison of the DpnM structure and sequences of group alpha DNA Mtases indicates that the group is a genetically related family. Structural comparisons show DpnM to be most similar to a small-molecule Mtase and then to macromolecular Mtases, although several dehydrogenases show greater similarity than one DNA Mtase. CONCLUSIONS:. DpnM, and by extension the DpnM family or group alpha Mtases, contains the consensus fold and AdoMet-binding motifs found in most Mtases. Structural considerations suggest that macromolecular Mtases evolved from small-molecule Mtases, with different groups of DNA Mtases evolving independently. Mtases may have evolved from dehydrogenases. Comparison of these enzymes indicates that in protein evolution, the structural fold is most highly conserved, then function and lastly sequence.

Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.,Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA Structure. 1998 Dec 15;6(12):1563-75. PMID:9862809^[1]

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

References

↑ Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA. Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine. Structure. 1998 Dec 15;6(12):1563-75. PMID:9862809

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dpm"

@@ Line 1: / Line 1: @@
 ==DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE==
-<StructureSection load='2dpm' size='340' side='right' caption='[[2dpm]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2dpm' size='340' side='right'caption='[[2dpm]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dpm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DPM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dpm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DPM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPNM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPNM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</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='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='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=2dpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpm OCA], [http://pdbe.org/2dpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dpm RCSB], [http://www.ebi.ac.uk/pdbsum/2dpm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpm 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=2dpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dpm OCA], [https://pdbe.org/2dpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dpm RCSB], [https://www.ebi.ac.uk/pdbsum/2dpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dpm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MTD21_STREE MTD21_STREE]] This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands, and protects the DNA from cleavage by the DpnII endonuclease.
+[[https://www.uniprot.org/uniprot/MTD21_STREE MTD21_STREE]] This methylase recognizes the double-stranded sequence GATC, causes specific methylation on A-2 on both strands, and protects the DNA from cleavage by the DpnII endonuclease.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 34: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Cerritelli, S]]
 [[Category: Korszun, Z R]]

2dpm

From Proteopedia

Revision as of 11:34, 10 February 2021

DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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