1yfj
From Proteopedia
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|PDB= 1yfj |SIZE=350|CAPTION= <scene name='initialview01'>1yfj</scene>, resolution 2.69Å | |PDB= 1yfj |SIZE=350|CAPTION= <scene name='initialview01'>1yfj</scene>, resolution 2.69Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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/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] | + | |ACTIVITY= <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> |
| - | |GENE= DAM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= DAM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1q0s|1Q0S]], [[1q0t|1Q0T]], [[1yf3|1YF3]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfj OCA], [http://www.ebi.ac.uk/pdbsum/1yfj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yfj RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1YFJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 1YFJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFJ OCA]. |
==Reference== | ==Reference== | ||
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase., Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X, Cell. 2005 May 6;121(3):349-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15882618 15882618] | Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase., Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X, Cell. 2005 May 6;121(3):349-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15882618 15882618] | ||
| - | [[Category: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Site-specific DNA-methyltransferase (adenine-specific)]] | [[Category: Site-specific DNA-methyltransferase (adenine-specific)]] | ||
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[[Category: Jeltsch, A.]] | [[Category: Jeltsch, A.]] | ||
[[Category: Liebert, K.]] | [[Category: Liebert, K.]] | ||
| - | + | [[Category: dna,protein-dna complex]] | |
| - | + | ||
| - | + | ||
| - | [[Category: dna]] | + | |
[[Category: methyltransferase]] | [[Category: methyltransferase]] | ||
| - | [[Category: protein-dna complex]] | ||
[[Category: t4dam]] | [[Category: t4dam]] | ||
| - | ''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 01:05:39 2008'' |
Revision as of 22:05, 30 March 2008
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| , resolution 2.69Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Gene: | DAM (Enterobacteria phage T4) | ||||||
| Activity: | Site-specific DNA-methyltransferase (adenine-specific), with EC number 2.1.1.72 | ||||||
| Related: | 1Q0S, 1Q0T, 1YF3
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact
Overview
DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.
About this Structure
1YFJ is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase., Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X, Cell. 2005 May 6;121(3):349-61. PMID:15882618
Page seeded by OCA on Mon Mar 31 01:05:39 2008
