1K61

MATALPHA2 HOMEODOMAIN BOUND TO DNA

Summary for 1K61

• Entry DOI: 10.2210/pdb1k61/pdb
• Related: 1APL 1MNM 1YRN
• Descriptor: 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP*GP*C)-3', 5'-D(*(5IU)P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP*G)-3', Mating-type protein alpha-2, ... (4 entities in total)
• Functional Keywords: protein-dna complex, homeodomain, hoogsteen base pair, transcription-dna complex, transcription/dna
• Total number of polymer chains: 6
• Total formula weight: 42095.80

Authors

Aishima, J.,Gitti, R.K.,Noah, J.E.,Gan, H.H.,Schlick, T.,Wolberger, C. (deposition date: 2001-10-14, release date: 2002-12-11, Last modification date: 2023-08-16)

Primary citation

Aishima, J.,Gitti, R.K.,Noah, J.E.,Gan, H.H.,Schlick, T.,Wolberger, C.
A Hoogsteen base pair embedded in undistorted B-DNA
NUCLEIC ACIDS RES., 30:5244-5252, 2002

PubMed Abstract: Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 A resolution structure of the MATalpha2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson-Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain-DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein-DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.

PubMed: 12466549
DOI: 10.1093/nar/gkf661

Experimental method

X-RAY DIFFRACTION (2.1 Å)