PDBsum entry 2nxq

Metal binding protein

PDB id: 2nxq

Contents

Protein chains

66 a.a. *

Ligands

ACT ×5

Metals

_CA ×4

Waters ×31

* Residue conservation analysis

PDB id:

2nxq

Name:

Metal binding protein

Title:

Crystal structure of calcium binding protein 1 from entamoeba histolytica: a novel arrangement of ef hand motifs

Structure:

Calcium-binding protein. Chain: a, b. Synonym: cabp. Engineered: yes

Source:

Entamoeba histolytica. Organism_taxid: 294381. Strain: hm-1:imss. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.40Å R-factor: 0.258 R-free: 0.282

Authors:

S.Kumar,N.Padhan,N.Alam,S.Gourinath

Key ref:

S.Kumar et al. (2007). Crystal structure of calcium binding protein-1 from Entamoeba histolytica: a novel arrangement of EF hand motifs. Proteins, 68, 990-998. PubMed id: 17554780 DOI: 10.1002/prot.21455

Date:

18-Nov-06 Release date: 21-Aug-07

Protein chains

P38505  (CABP1_ENTH1) -  Calcium-binding protein 1 from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)

Seq: 134 a.a.

Struc: 66 a.a.

DOI no: 10.1002/prot.21455

Proteins 68:990-998 (2007)

PubMed id: 17554780

Crystal structure of calcium binding protein-1 from Entamoeba histolytica: a novel arrangement of EF hand motifs.

S.Kumar, N.Padhan, N.Alam, S.Gourinath.

ABSTRACT

Calcium plays a pivotal role in the pathogenesis of amoebiasis, a major disease caused by Entamoeba histolytica. Several EF-hand containing calcium-binding proteins (CaBPs) have been identified from E. histolytica. Even though these proteins have very high sequence similarity, they bind to different target proteins in a Ca2+ dependent manner, leading to different functional pathways (Yadava et al., Mol Biochem Parasito 1997;84:69-82; Chakrabarty et al., J Biol Chem 2004;279:12898-12908) The crystal structure of the Entamoeba histolytica calcium binding protein-1 (EhCaBP1) has been determined at 2.4 A resolution. The crystals were grown using MPD as precipitant and they belong to P6(3) space group with unit cell parameters of a = 95.25 A, b = 95.25 A, c = 64.99 A. Only two out of the four expected EF hand motifs could be modeled into the electron density map and the final model refined to R factor of 25.6% and Free_R of 28%. Unlike CaM, the first two EF hand motifs in EhCaBP1 are connected by a long helix and form a dumbbell shaped structure. Owing to domain swapping oligomerization three EhCaBP1 molecules interact in a head to tail manner to form a triangular trimer. This arrangement allows the EF-hand motif of one molecule to interact with that of an adjacent molecule to form a two EF-hand domain similar to that seen in the N-terminal domain of the NMR structure of CaBP1, calmodulin and troponin C. The oligomeric state of EhCaBP1 results in reduced flexibility between domains and may be responsible for the more limited set of targets recognized by EhCaBP1.

Selected figure(s)

Figure 1.
Figure 1. Structure of Calcium binding protein 1 from E. histolytica (EhCaBP1). (A) Schematic representation of CaBP1, showing calcium binding loops (CaBL) with residue numbers (CaBL1 in blue and CaBL2 in red). The central linker region of the protein is displayed in orange, which has three glycines imparting flexibility to the molecule. (B) Structure of N-terminal half of the CaBP1 traced in the crystal structure is displayed as a ribbon diagram generated by PyMOL,[25] calcium's (grey) are shown as spheres in two EF hand motifs. Two EF hand motifs are connected by straight helix (green). (C) Connecting helix between two EF hand motifs is well defined. Part of the helix is shown with 2Fo-Fc electron density map at 2 .

Figure 5.
Figure 5. A superposition of CaM on trimer of EhCaBP1 that reveals the similarity of the assembled domain to CaM N-terminal domain. (A) The CaM N-terminal domain (red) was superposed (by least square fit) on assembled domain of EF1 of one molecule (light blue) and EF2 of neighboring molecule (purple) highlights the domain similarity. The distance between N-terminal and C-terminal domains in CaM is approximately equal to the distance between the two assembled domains of EhCaBP1 trimer. But the linker helix in CaM bends about 15° and thus C-terminal domain of CaM do not overlap with the next assembled domain. (B). Magnified view of CaM N-terminal domain (red) superposed on assembled domain of EhCaBP1 trimer (EF1 in blue, EF2 in purple).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 990-998) copyright 2007.

Figures were selected by an automated process.