1yo5: Difference between revisions

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|PDB= 1yo5 |SIZE=350|CAPTION= <scene name='initialview01'>1yo5</scene>, resolution 2.00&Aring;
|PDB= 1yo5 |SIZE=350|CAPTION= <scene name='initialview01'>1yo5</scene>, resolution 2.00&Aring;
|SITE=  
|SITE=  
|LIGAND=  
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
|ACTIVITY=  
|ACTIVITY=  
|GENE= PDEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
|GENE= PDEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
|DOMAIN=
|RELATEDENTRY=
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yo5 OCA], [http://www.ebi.ac.uk/pdbsum/1yo5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yo5 RCSB]</span>
}}
}}


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==Overview==
==Overview==
PDEF, a prostate epithelial specific transcription factor, is a member of the Ets family of DNA binding proteins. Here we report a 2.0 A crystal structure of the PDEF Ets domain in complex with a natural, high-affinity DNA binding site in the promoter/enhancer region of the human prostate specific antigen gene. Comparison of the PDEF-DNA complex with other Ets complexes revealed key features that are shared among Ets members, as well as important differences in substrate specification at both the "GGA" core and the flanking regions of the DNA site. The combination of the serine residue at position 308 and the glutamine at position 311 explains the previous observation that the PDEF binds preferentially to a thymine at the +4 position of its binding site. Despite the common essential features that are shared among Ets members, PDEF demonstrates distinct patterns of interactions at different positions of DNA in achieving sequence specific recognition. Collectively, the common and unique interactions with both the DNA bases and the backbone phosphates lead to substrate specificity and individual preference for certain DNA sites.
PDEF, a prostate epithelial specific transcription factor, is a member of the Ets family of DNA binding proteins. Here we report a 2.0 A crystal structure of the PDEF Ets domain in complex with a natural, high-affinity DNA binding site in the promoter/enhancer region of the human prostate specific antigen gene. Comparison of the PDEF-DNA complex with other Ets complexes revealed key features that are shared among Ets members, as well as important differences in substrate specification at both the "GGA" core and the flanking regions of the DNA site. The combination of the serine residue at position 308 and the glutamine at position 311 explains the previous observation that the PDEF binds preferentially to a thymine at the +4 position of its binding site. Despite the common essential features that are shared among Ets members, PDEF demonstrates distinct patterns of interactions at different positions of DNA in achieving sequence specific recognition. Collectively, the common and unique interactions with both the DNA bases and the backbone phosphates lead to substrate specificity and individual preference for certain DNA sites.
==Disease==
Known diseases associated with this structure: Alzheimer disease, type 3 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]], Alzheimer disease, type 3, with spastic paraparesis and apraxia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]], Alzheimer disease, type 3, with spastic paraparesis and unusual plaques OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]], Cardiomyopathy, dilated, 1U OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]], Dementia, frontotemporal OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]], Pick disease OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104311 104311]]


==About this Structure==
==About this Structure==
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[[Category: Said, M.]]
[[Category: Said, M.]]
[[Category: Wang, Y.]]
[[Category: Wang, Y.]]
[[Category: ets; protein-dna complex; double helix]]
[[Category: double helix]]
[[Category: et]]
[[Category: protein-dna complex]]


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