PDBsum entry 2be4

Structural genomics, unknown function

PDB id: 2be4

Contents

Protein chain

270 a.a. *

Waters ×240

* Residue conservation analysis

PDB id:

2be4

Name:

Structural genomics, unknown function

Title:

X-ray structure an ef-hand protein from danio rerio dr.36843

Structure:

Hypothetical protein loc449832. Chain: a. Engineered: yes

Source:

Danio rerio. Zebrafish. Organism_taxid: 7955. Gene: dr.36843, bc083168. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.179 R-free: 0.253

Authors:

G.E.Wesenberg,G.N.Phillips Jr.,B.W.Han,E.Bitto,C.A.Bingman,E.Bae, Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

E.Bitto et al. (2009). X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor. Proteins, 76, 477-483. PubMed id: 19241471 DOI: 10.1002/prot.22362

Date:

21-Oct-05 Release date: 01-Nov-05

Protein chain

Q5XJX1  (SEGN_DANRE) -  Secretagogin from Danio rerio

Seq: 272 a.a.

Struc: 270 a.a.

DOI no: 10.1002/prot.22362

Proteins 76:477-483 (2009)

PubMed id: 19241471

X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor.

E.Bitto, C.A.Bingman, L.Bittova, R.O.Frederick, B.G.Fox, G.N.Phillips.

ABSTRACT

Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hexa-EF-hand protein that is highly expressed in pancreatic islet of Langerhans and neuroendocrine cells and may play a role in the trafficking of secretory granules. We present the X-ray structure of Danio rerio secretagogin, which is 73% identical to human secretagogin, in calcium-free form at 2.1-A resolution. Secretagogin consists of the three globular domains each of which contains a pair of EF-hand motifs. The domains are arranged into a V-shaped molecule with a distinct groove formed at the interface of the domains. Comparison of the secretagogin structure with the solution structure of calcium-loaded calbindin D(28K) revealed a striking difference in the spatial arrangement of their domains, which involves approximately 180 degrees rotation of the first globular domain with respect to the module formed by the remaining domains. Proteins 2009. (c) 2009 Wiley-Liss, Inc.

Selected figure(s)

Figure 1.
Figure 1. The X-ray crystal structure of D. rerio secretagogin. A: Secretagogin monomer consists of six EF-hand motifs arranged in pairs to form three globular domains (rendered consecutively in red, yellow, and cyan). Linkers L1 and L2, highlighted in green, connect the individual domains. The apposed metal binding loops form antiparallel -sheet on the outer surface of the V-shaped molecule. The helices of the individual EF-hand motifs are labeled for clarity. B: A stereo view of C -trace of the superposed domains I, II, and III (red, yellow, and cyan, respectively) of secretagogin. The topologically equivalent motifs EF1, EF3, and EF5 overlap well, except for the Ca^2+-binding loop which adopts the open, Ca^2+-ready conformation in EF5-hand (cyan arrow) and closed, Ca^2+-free conformation in EF1 and EF3 motifs. The EF2 hand differs from all the remaining EF-hands due to a break at Met63 in the helix E2 (red arrow). C: A stereo image of the calcium-binding loop in EF5-hand motif of D. rerio secretagogin. A final 2mF[o]-DF[c] electron density map (blue mesh) is contoured at 1.2 level. The refined protein model is shown in sticks. Residues of the calcium-binding motif at positions 1 (Asp206), 3 (Ser208), 5 (Thr210), 7 (Ala212), and 12 (Glu217) are labeled for clarity. A symmetry molecule of secretagogin from the crystalline lattice contributes Lys138 (cyan sticks), which mimics the positively charged calcium ion and stabilizes the loop in Ca^2+-ready -like conformation.

Figure 3.
Figure 3. D. rerio secretagogin and rat calbindin D[28K] have different quarternary domain arrangement. The domain II and III of D. rerio secretagogin (red) were superposed with the corresponding region of rat calbindin D[28K] (blue; PDB ID 2f33). In the resulting overlay, the domain I of secretagogin is rotated by almost 180° with respect to the core formed by domains II and III in both proteins. The green arrow points to the point from which structures diverge.

The above figures are reprinted from an Open Access publication published by John Wiley & Sons, Inc.: Proteins (2009, 76, 477-483) copyright 2009.

Figures were selected by an automated process.