2KVF

Structure of the three-Cys2His2 domain of mouse testis zinc finger protein

Summary for 2KVF

• Entry DOI: 10.2210/pdb2kvf/pdb
• Related: 2KVG 2KVH
• Descriptor: Zinc finger and BTB domain-containing protein 32, ZINC ION (2 entities in total)
• Functional Keywords: protein/dna, metal-binding, zinc-finger, transcription
• Biological source: Mus musculus (mouse)
• Total number of polymer chains: 1
• Total formula weight: 3413.33

Authors

Chou, C.-C.,Lou, Y.-C.,Chen, C. (deposition date: 2010-03-15, release date: 2010-04-14, Last modification date: 2024-05-01)

Primary citation

Chou, C.-C.,Lou, Y.-C.,Tang, T.K.,Chen, C.
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
Proteins, 78:2202-2212, 2010

PubMed Abstract: The C-terminal three-Cys(2)His(2) zinc-finger domain (TZD) of mouse testis zinc-finger protein binds to the 5'-TGTACAGTGT-3' at the Aie1 (aurora-C) promoter with high specificity. Interestingly, the primary sequence of TZD is unique, possessing two distinct linkers, TGEKP and GAAP, and distinct residues at presumed DNA binding sites at each finger, especially finger 3. A K(d) value of approximately 10(-8) M was obtained from surface plasmon resonance analysis for the TZD-DNA complex. NMR structure of the free TZD showed that each zinc finger forms a typical beta beta alpha fold. On binding to DNA, chemical shift perturbations and the R(2) transverse relaxation rate in finger 3 are significantly smaller than those in fingers 1 and 2, which indicates that the DNA binding affinity in finger 3 is weaker. Furthermore, the shift perturbations between TZD in complex with the cognate DNA and its serial mutants revealed that both ADE7 and CYT8, underlined in 5'-ATATGTACAGTGTTAT-3', are critical in specific binding, and the DNA binding in finger 3 is sequence independent. Remarkably, the shift perturbations in finger 3 on the linker mutation of TZD (GAAP mutated to TGEKP) were barely detected, which further indicates that finger 3 does not play a critical role in DNA sequence-specific recognition. The complex model showed that residues important for DNA binding are mainly located on positions -1, 2, 3, and 6 of alpha-helices in fingers 1 and 2. The DNA sequence and nonsequence-specific bindings occurring simultaneously in TZD provide valuable information for better understanding of protein-DNA recognition.

PubMed: 20544958
DOI: 10.1002/prot.22732

Experimental method

SOLUTION NMR