2zcj
From Proteopedia
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|PDB= 2zcj |SIZE=350|CAPTION= <scene name='initialview01'>2zcj</scene>, resolution 2.75Å | |PDB= 2zcj |SIZE=350|CAPTION= <scene name='initialview01'>2zcj</scene>, resolution 2.75Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_(cytosine-5-)-methyltransferase DNA (cytosine-5-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.37 2.1.1.37] </span> |
|GENE= hhaIM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=735 Haemophilus parahaemolyticus]) | |GENE= hhaIM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=735 Haemophilus parahaemolyticus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2hr1|2HR1]], [[2z6u|2Z6U]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zcj OCA], [http://www.ebi.ac.uk/pdbsum/2zcj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2zcj RCSB]</span> | ||
}} | }} | ||
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[[Category: Reich, N O.]] | [[Category: Reich, N O.]] | ||
[[Category: Shieh, F K.]] | [[Category: Shieh, F K.]] | ||
| - | [[Category: SAH]] | ||
[[Category: 3-layer sandwich]] | [[Category: 3-layer sandwich]] | ||
[[Category: alpha and beta]] | [[Category: alpha and beta]] | ||
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[[Category: transferase/dna complex]] | [[Category: transferase/dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:20:20 2008'' |
Revision as of 02:20, 31 March 2008
| |||||||
| , resolution 2.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | hhaIM (Haemophilus parahaemolyticus) | ||||||
| Activity: | DNA (cytosine-5-)-methyltransferase, with EC number 2.1.1.37 | ||||||
| Related: | 2HR1, 2Z6U
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy
Overview
The role of Glu119 in S-adenosyl-L-methionine-dependent DNA methyltransferase M.HhaI-catalyzed DNA methylation was studied. Glu119 belongs to the highly conserved Glu/Asn/Val motif found in all DNA C5-cytosine methyltransferases, and its importance for M.HhaI function remains untested. We show that formation of the covalent intermediate between Cys81 and the target cytosine requires Glu119, since conversion to Ala, Asp or Gln lowers the rate of methyl transfer 10(2)-10(6) fold. Further, unlike the wild-type M.HhaI, these mutants are not trapped by the substrate in which the target cytosine is replaced with the mechanism-based inhibitor 5-fluorocytosine. The DNA binding affinity for the Glu119Asp mutant is decreased 10(3)-fold. Thus, the ability of the enzyme to stabilize the extrahelical cytosine is coupled directly to tight DNA binding. The structures of the ternary protein/DNA/AdoHcy complexes for both the Glu119Ala and Glu119Gln mutants (2.70 A and 2.75 A, respectively) show that the flipped base is positioned nearly identically with that observed in the wild-type M.HhaI complex. A single water molecule in the Glu119Ala structure between Ala119 and the extrahelical cytosine N3 is lacking in the Glu119Gln and wild-type M.HhaI structures, and most likely accounts for this mutant's partial activity. Glu119 has essential roles in activating the target cytosine for nucleophilic attack and contributes to tight DNA binding.
About this Structure
2ZCJ is a Protein complex structure of sequences from Haemophilus parahaemolyticus. Full crystallographic information is available from OCA.
Reference
AdoMet-dependent methyl-transfer: Glu119 is essential for DNA C5-cytosine methyltransferase M.HhaI., Shieh FK, Reich NO, J Mol Biol. 2007 Nov 9;373(5):1157-68. Epub 2007 Aug 19. PMID:17897676
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