Three-dimensional structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor.

W J Cook,S E Ealick,Y S Babu,J A Cox,S Vijay-Kumar

doi:10.1016/s0021-9258(18)52484-4

Abstract

The three-dimensional structure of a sarcoplasmic Ca2(+)-binding protein from the sandworm Nereis diversicolor has been determined at 3.0 A resolution using multiple isomorphous replacement techniques. The NH2-terminal half of the molecule contains one variant Ca2(+)-binding domain with a novel helix-loop-helix conformation and one Ca2(+)-binding domain that is no longer functional because of amino acid changes. The overall conformation of this pair of domains is different from any previously described Ca2(+)-binding protein. The COOH-terminal half of the protein contains two Ca2(+)-binding domains with the usual helix-loop-helix configuration and is similar to calmodulin and troponin C. Unlike calmodulin or troponin C, there is no exposed alpha-helix connecting the two halves of the molecule, so the overall structure is much more compact.

Highlights

From the Departments of $Pathology, IIPharmacology, and §§Biochemistry and §Centerfor Macromolecular Crystallography, University of Alabama at Birmingham, Birmingham, Alabama 35294 and the $$DepartmeofntBiochemistry, Universityof Geneva, CH11211 Geneva 4, Switzerland
The COOH-terminal half of the protein contains two Ca2+-bindingdomains with the usual helixloop-helix configuration and is similar to calmodulin the sequence corresponding to domain I1 has had a number of amino acid replacements and deletions and does not bind Ca2+.We have previously reported a preliminary crystallographic study of Nereis SCP (21)
We report here the determinatio? of the three-dimensional structure of Nereis SCP at 3.0 A resolutionemployingmultipleisomorphous and troponin C

Summary

Relative OccuDancv

Helices in the molecule could beseen clearly in this map. One of the two polypeptide chains was traced and aligned with the amino acid sequencewith the aid of the graphics program FRODO (14).The other molecule wasgenerated using the noncrystallographic symmetry. The coordinates were refined using PROLSQ (15), and one molecule was refit to the MIR/solvent flattened map that had been averaged using the noncrystallographic 2-fold axis. After refinement with PROLSQ, the entire model underwent two cycles of refitting using anOMITmap (16) and refining with PROLSQ. The current R-factor at 3.0 A is 0.22. The 0-carbon coordinates for Nereis SCP have been deposited with the Protein Data Bank, Chemistry Department, Brookhaven National Laboratory, Upton, NY

RESULTS

Troponin C

DISCUSSION

Findings

The interhelical angles between helices on adjacent domains