3SNZ

Crystal structure of a mutant W39D of a betagamma-crystallin domain from Clostridium beijerinckii

Summary for 3SNZ

• Entry DOI: 10.2210/pdb3snz/pdb
• Related: 3I9H 3IAJ 3SNY 3SO0 3SO1
• Descriptor: Clostrillin, CALCIUM ION (3 entities in total)
• Functional Keywords: calcium-bound betagamma-crystallin, metal binding protein
• Biological source: Clostridium beijerinckii
• Total number of polymer chains: 1
• Total formula weight: 10702.66

Authors

Srivastava, S.S.,Sankaranarayanan, R. (deposition date: 2011-06-29, release date: 2011-11-16, Last modification date: 2023-11-01)

Primary citation

Mishra, A.,Suman, S.K.,Srivastava, S.S.,Sankaranarayanan, R.,Sharma, Y.
Decoding the molecular design principles underlying Ca(2+) binding to beta gamma-crystallin motifs
J.Mol.Biol., 415:75-91, 2012

PubMed Abstract: Numerous proteins belonging to the recently expanded βγ-crystallin superfamily bind Ca(2+) at the double-clamp N/D-N/D-X(1)-X(2)-S/T-S motif. However, there have been no attempts to understand the intricacies involving Ca(2+) binding, such as the determinants of Ca(2+)-binding affinity and their contributions to gain in stability. This work is an in-depth analysis of understanding the modes and determinants of Ca(2+) binding to βγ-crystallin motifs. We have performed extensive naturally occurring substitutions from related proteins on the βγ-crystallin domains of flavollin, a low-affinity Ca(2+)-binding protein, and clostrillin, a moderate-affinity protein. We monitored the consequences of these modifications on Ca(2)(+) binding by isothermal titration calorimetry, thermal stability and conformational and crystal structure analyses. We demonstrate that Ca(2)(+) binding to the two sites of a βγ-domain is interdependent and that the presence of Arg at the fifth position disables a site. A change from Thr to Ser, or vice versa, influences Ca(2+)-binding affinity, highlighting the basis of diversity found in these domains. A subtle change in the first site has a greater influence on Ca(2)(+) binding than a similar alteration in the second site. Thus, the second site is more variable in nature. Replacing an acidic or hydrophobic residue in a binding site alters the Ca(2+)-binding properties drastically. While it appears from their binding site sequence that these domains have evolved randomly, our examination illustrates the subtlety in the design of these modules. Decoding such design schemes would aid in our understanding of the functional themes underlying differential Ca(2)(+) binding and in predicting these in emerging sequence information.

PubMed: 22099475
DOI: 10.1016/j.jmb.2011.10.037

Experimental method

X-RAY DIFFRACTION (2 Å)