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1cyz
From Proteopedia
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|PDB= 1cyz |SIZE=350|CAPTION= <scene name='initialview01'>1cyz</scene> | |PDB= 1cyz |SIZE=350|CAPTION= <scene name='initialview01'>1cyz</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=AR1:(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM'>AR1</scene> | + | |LIGAND= <scene name='pdbligand=AR1:(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM'>AR1</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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1b0s|1B0S]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cyz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cyz OCA], [http://www.ebi.ac.uk/pdbsum/1cyz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cyz RCSB]</span> | ||
}} | }} | ||
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[[Category: Wang, A H.J.]] | [[Category: Wang, A H.J.]] | ||
[[Category: Yang, X L.]] | [[Category: Yang, X L.]] | ||
| - | [[Category: AR1]] | ||
[[Category: t:g recognized by im/im pair in the dna minor groove]] | [[Category: t:g recognized by im/im pair in the dna minor groove]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:31:14 2008'' |
Revision as of 16:31, 30 March 2008
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| Ligands: | , , , , | ||||||
| Related: | 1B0S
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX
Overview
The T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences may be aided by studying the structural perturbation of DNA caused by a T:G base pair and by specific probing of the mismatch using small molecular ligands. We have shown previously that AR-1-144, a tri-imidazole (Im-Im-Im) minor groove binder, recognizes the sequence CCGG. NMR structural analysis of the symmetric 2:1 complex of AR-1-144 and GAACCGGTTC revealed that each AR-1-144 binds to four base pairs with the guanine N2 amino group forming a bifurcated hydrogen bond to a side-by-side Im/Im pair. We predicted that the free G-N2 amino group in a T:G wobble base pair can form two individual hydrogen bonds to a side-by-side Im/Im pair. Thus an Im/Im pair may be a good recognition motif for a T:G base pair in DNA. Cooperative and tight binding of an AR-1-144 homodimer to GAACTGGTTC permits a detailed structural analysis by 2D NOE NMR refinement and the refined structure confirms our prediction. Surprisingly, AR-1-144 does not bind to GAATCGGTTC. We further show that both the Im-Im-Im/Im-Py-Im heterodimer and the Im-Im-Im/Im-Im-Im homodimer bind strongly to the CACGGGTC + GACTCGTG duplex. These results together suggest that an Im/Im pair can specifically recognize a single T:G mismatch. Our results may be useful in future design of molecules (e.g. linked dimers) that can recognize a single T:G mismatch with specificity.
About this Structure
1CYZ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs., Yang XL, Hubbard RB, Lee M, Tao ZF, Sugiyama H, Wang AH, Nucleic Acids Res. 1999 Nov 1;27(21):4183-90. PMID:10518609
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