3I9H

Crystal structure of a betagamma-crystallin domain from Clostridium beijerinckii

Summary for 3I9H

• Entry DOI: 10.2210/pdb3i9h/pdb
• Related: 1NPS 3HZB
• Descriptor: Beta and gamma crystallin, CALCIUM ION (3 entities in total)
• Functional Keywords: calcium-bound betagamma-crystallin, metal binding protein
• Biological source: Clostridium beijerinckii (Clostridium acetobutylicum)
• Total number of polymer chains: 8
• Total formula weight: 79190.94

Authors

Aravind, P.,Sankaranarayanan, R. (deposition date: 2009-07-11, release date: 2009-12-01, Last modification date: 2023-11-01)

Primary citation

Aravind, P.,Mishra, A.,Suman, S.K.,Jobby, M.K.,Sankaranarayanan, R.,Sharma, Y.
betagamma-Crystallin superfamily contains a universal motif for binding calcium.
Biochemistry, 2009

PubMed Abstract: The betagamma-crystallin superfamily consists of evolutionarily related proteins with domain topology similar to lens beta- and gamma-crystallins, formed from duplicated Greek key motifs. Ca(2+) binding was found in a few betagamma-crystallin members earlier, although its prevalence and diversity as inherent molecular properties among members of the superfamily are not well studied. To increase our understanding of Ca(2+) binding in various betagamma-crystallins, we undertook comprehensive structural and Ca(2+)-binding studies of seven members of the superfamily from bacteria, archaea, and vertebrates, including determination of high-resolution crystal structures of three proteins. Our structural observations show that the determinants of Ca(2+) coordination remain conserved in the form of an N/D-N/D-#-I-S/T-S motif in all domains. However, binding of Ca(2+) elicits varied physicochemical responses, ranging from passive sequestration to active stabilization. The motif in this superfamily is modified in some members like lens crystallins where Ca(2+)-binding abilities are partly or completely compromised. We show that reduction or loss of Ca(2+) binding in members of the superfamily, particularly in vertebrates, is due to the selective presence of unfavorable amino acids (largely Arg) at key Ca(2+)-ligation positions and that engineering of the canonical Ca(2+)-binding residues can confer binding activity on an otherwise inactive domain. Through this work, we demonstrate that betagamma-crystallins with the N/D-N/D-#-I-S/T-S motif form an extensive set of Ca(2+)-binding proteins prevalent in all of the three kingdoms of life.

PubMed: 19921810
DOI: 10.1021/bi9017076

Experimental method

X-RAY DIFFRACTION (2 Å)