PDBsum entry: 1p5s

Cytokine

PDB id: 1p5s

Contents

Protein chain

159 a.a. *

Metals

_HG ×4

Waters ×145

* Residue conservation analysis

PDB id:

1p5s

Name:

Cytokine

Title:

Structure and function of the calponin-homology domain of an iqgap protein from schizosaccharomyces pombe

Structure:

Ras gtpase-activating-like protein rng2. Chain: a. Fragment: calponin-homology domain. Synonym: ring assembly protein 2. Engineered: yes

Source:

Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: rng2 or spac4f8.13c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.22Å R-factor: 0.199 R-free: 0.246

Authors:

C.H.Wang,M.K.Balasubramanian,T.Dokland

Key ref:

C.H.Wang et al. (2004). Structure, crystal packing and molecular dynamics of the calponin-homology domain of Schizosaccharomyces pombe Rng2. Acta Crystallogr D Biol Crystallogr, 60, 1396-1403. PubMed id: 15272162 DOI: 10.1107/S0907444904012983

Date:

28-Apr-03 Release date: 11-May-04

Protein chain

O14188  (RNG2_SCHPO) -  Ras GTPase-activating-like protein rng2

Seq: 1489 a.a.

Struc: 159 a.a.

DOI no: 10.1107/S0907444904012983

Acta Crystallogr D Biol Crystallogr 60:1396-1403 (2004)

PubMed id: 15272162

Structure, crystal packing and molecular dynamics of the calponin-homology domain of Schizosaccharomyces pombe Rng2.

C.H.Wang, M.K.Balasubramanian, T.Dokland.

ABSTRACT

Schizosaccharomyces pombe Rng2 is an IQGAP protein that is essential for the assembly of an actomyosin ring during cytokinesis. Rng2 contains an amino-terminal calponin-homology (CH) domain, 11 IQ repeats and a RasGAP-homology domain. CH domains are known mainly for their ability to bind F-actin, although they have other ligands in vivo and there are only few examples of actin-binding single CH domains. The structures of several CH domains have already been reported, but this is only the third report of an actin-binding protein that contains a single CH domain (the structures of calponin and EB1 have been reported previously). The 2.21 A resolution crystal structure of the amino-terminal 190 residues of Rng2 from Br- and Hg-derivatives includes 40 residues (150-190) carboxyl-terminal to the CH domain that resemble neither the extended conformation seen in utrophin, nor the compact conformation seen in fimbrin, although residues 154-160 form an unstructured coil which adopts a substructure similar to dystrophin residues 240-246 in the carboxyl-terminal portion of the CH2 domain. This region wraps around the stretch of residues that would be equivalent to the proposed actin-binding site ABS1 and ABS2 from dystrophin. This distinctive feature is absent from previously published CH-domain structures. Another feature revealed by comparing the two derivatives is the presence of two loop conformations between Tyr92 and Arg99.

Selected figure(s)

Figure 1.
Figure 1 Domain organization within Rng2. Domain boundaries (numbers in red) were defined by performing a global search across a Pfam HMM library (Eddy, 1998[Eddy, S. R. (1998). Bioinformatics, 14, 755-763.]).

Figure 2.
Figure 2 Structure of Rng2[1-190]. (a) Ribbon representation of the crystal structure of Rng2[1-190]shown in two orientations with a relative rotation of 180°. Br atoms are represented by spheres coloured according to B factors (blue to red denoting lower to higher values). The amino- and carboxyl-terminal residues are labelled together with -helices a1-a7 and 3[10]-helices h1-h3. For comparison purposes, the region corresponding to actin-binding sites ABS1 (a1) and ABS2 (h2-a6) of dystrophin CH1 domain (Norwood et al., 2000[Norwood, F. L. M., Sutherland-Smith, A. J., Keep, N. H. & Kendrick-Jones, J. (2000). Structure, 8, 481-491.]) are highlighted in green and blue, respectively. The 40 residues carboxyl-terminal to the CH domain (150-190) are highlighted in red. (b) C^ -backbone superposition of the CH domains from the Br-derivative of Rng2 CH (pink), Hg-derivative of Rng2 CH (plum), dystrophin CH1 (red), dystrophin CH2 (orange-red), calponin CH (orange), EB1 CH (yellow), fimbrin CH1-1 (yellow-green), fimbrin CH1-2 (green-yellow), utrophin CH1 (green), utrophin CH2 (cyan), plectin CH1 (dark cyan), plectin CH2 (blue) and -spectrin CH2 (blue-violet). (c) C^ backbone superposition of the four core -helices belonging to the Br-derivative of Rng2[1-190] CH (pink), dystrophin CH1 (red), calponin CH (orange) and plectin CH2 (blue) domains. Orientations in (a), (b) and (c) are the same.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1396-1403) copyright 2004.

Figures were selected by an automated process.