3QD7

Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli

Summary for 3QD7

• Entry DOI: 10.2210/pdb3qd7/pdb
• Descriptor: Uncharacterized protein ydaL (2 entities in total)
• Functional Keywords: alpha/beta/alpha fold, endonuclease, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 15442.69

Authors

Gui, W.J.,Qu, Q.H.,Chen, Y.Y.,Wang, M.,Zhang, X.E.,Bi, L.J.,Jiang, T. (deposition date: 2011-01-18, release date: 2011-06-22, Last modification date: 2024-03-20)

Primary citation

Gui, W.J.,Qu, Q.H.,Chen, Y.Y.,Wang, M.,Zhang, X.E.,Bi, L.J.,Jiang, T.
Crystal structure of YdaL, a stand-alone small MutS-related protein from Escherichia coli.
J.Struct.Biol., 174:282-289, 2011

PubMed Abstract: Sequence homologs of the small MutS-related (Smr) domain, the C-terminal endonuclease domain of MutS2, also exist as stand-alone proteins. In this study, we report the crystal structure of a proteolyzed fragment of YdaL (YdaL₃₉-₁₇₅), a stand-alone Smr protein from Escherichia coli. In this structure, residues 86-170 assemble into a classical Smr core domain and are embraced by an N-terminal extension (residues 40-85) with an α/β/α fold. Sequence alignment indicates that the N-terminal extension is conserved among a number of stand-alone Smr proteins, suggesting structural diversity among Smr domains. We also discovered that the DNA binding affinity and endonuclease activity of the truncated YdaL₃₉-₁₇₅ protein were slightly lower than those of full-length YdaL₁-₁₈₇, suggesting that residues 1-38 may be involved in DNA binding.

PubMed: 21276852
DOI: 10.1016/j.jsb.2011.01.008

Experimental method

X-RAY DIFFRACTION (2.3 Å)