PDBsum entry 3so0

Metal binding protein

PDB id: 3so0

Contents

Protein chains

(+ 1 more) 86 a.a.

72 a.a.

Metals

_CA ×13

Waters ×381

PDB id:

3so0

Name:

Metal binding protein

Title:

Crystal structure of a mutant t41s of a betagamma-crystallin domain from clostridium beijerinckii

Structure:

Clostrillin. Chain: a, b, c, d, e, f, g, h. Fragment: betagamma-crystallin domain, unp residues 118-213. Synonym: beta and gamma crystallin. Engineered: yes. Mutation: yes

Source:

Clostridium beijerinckii. Organism_taxid: 290402. Strain: ncimb 8052. Gene: cbei_2825. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.93Å R-factor: 0.200 R-free: 0.238

Authors:

S.S.Srivastava,R.Sankaranarayanan

Key ref:

A.Mishra et al. (2012). Decoding the molecular design principles underlying Ca(2+) binding to βγ-crystallin motifs. J Mol Biol, 415, 75-91. PubMed id: 22099475

Date:

29-Jun-11 Release date: 16-Nov-11

Protein chains

A6LX94  (A6LX94_CLOB8) -  Beta and gamma crystallin from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)

Seq: 589 a.a.

Struc: 86 a.a.*

Protein chain

A6LX94  (A6LX94_CLOB8) -  Beta and gamma crystallin from Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052)

Seq: 589 a.a.

Struc: 72 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

J Mol Biol 415:75-91 (2012)

PubMed id: 22099475

Decoding the molecular design principles underlying Ca(2+) binding to βγ-crystallin motifs.

A.Mishra, S.K.Suman, S.S.Srivastava, R.Sankaranarayanan, Y.Sharma.

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.