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2MAM

Solution structure of the interdigitated double Tudor domain of RBBP1

Replaces:  2LCD
Summary for 2MAM
Entry DOI10.2210/pdb2mam/pdb
Related2LCC
NMR InformationBMRB: 17607
DescriptorAT-rich interactive domain-containing protein 4A (1 entity in total)
Functional Keywordsretinoblastoma binding protein 1, interdigitated double tudor domain, dna binding protein
Biological sourceHomo sapiens (human)
Cellular locationNucleus: P29374
Total number of polymer chains1
Total formula weight13172.86
Authors
Gong, W.,Feng, Y. (deposition date: 2013-07-15, release date: 2014-01-15, Last modification date: 2024-05-15)
Primary citationGong, W.,Wang, J.,Perrett, S.,Feng, Y.
Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.
J.Biol.Chem., 289:4882-4895, 2014
Cited by
PubMed Abstract: Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.
PubMed: 24379399
DOI: 10.1074/jbc.M113.501940
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

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