1yo5
From Proteopedia
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|PDB= 1yo5 |SIZE=350|CAPTION= <scene name='initialview01'>1yo5</scene>, resolution 2.00Å | |PDB= 1yo5 |SIZE=350|CAPTION= <scene name='initialview01'>1yo5</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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> |
|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. | ||
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| - | ==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: | + | [[Category: double helix]] |
| + | [[Category: et]] | ||
| + | [[Category: protein-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 01:15:17 2008'' |
Revision as of 22:15, 30 March 2008
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| , resolution 2.00Å | |||||||
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| Ligands: | , , , | ||||||
| Gene: | PDEF (Homo sapiens) | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site
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.
About this Structure
1YO5 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Analysis of the 2.0 A crystal structure of the protein-DNA complex of the human PDEF Ets domain bound to the prostate specific antigen regulatory site., Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, Ghosh D, Gulick AM, Biochemistry. 2005 May 17;44(19):7095-106. PMID:15882048
Page seeded by OCA on Mon Mar 31 01:15:17 2008
Categories: Homo sapiens | Single protein | Balderman, S. | Fayazi, Z. | Feng, L. | Ghosh, D. | Gulick, A M. | Liu, Y. | Said, M. | Wang, Y. | Double helix | Et | Protein-dna complex
