PDBsum entry 1hdf

Structural protein

PDB id: 1hdf

Contents

Protein chains

100 a.a. *

Metals

_CA ×4

Waters ×127

* Residue conservation analysis

PDB id:

1hdf

Name:

Structural protein

Title:

Evolution of the eye lens beta-gamma-crystallin domain fold

Structure:

Spherulin 3a. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Physarum polycephalum. Organism_taxid: 5791. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.239

Authors:

N.J.Clout,M.Kretschmar,R.Jaenicke,C.Slingsby

Key ref:

N.J.Clout et al. (2001). Crystal structure of the calcium-loaded spherulin 3a dimer sheds light on the evolution of the eye lens betagamma-crystallin domain fold. Structure, 9, 115-124. PubMed id: 11250196 DOI: 10.1016/S0969-2126(01)00573-1

Date:

13-Nov-00 Release date: 28-Dec-00

Protein chains

P09353  (SR3A_PHYPO) -  Spherulin-3A from Physarum polycephalum

Seq: 103 a.a.

Struc: 100 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/S0969-2126(01)00573-1

Structure 9:115-124 (2001)

PubMed id: 11250196

Crystal structure of the calcium-loaded spherulin 3a dimer sheds light on the evolution of the eye lens betagamma-crystallin domain fold.

N.J.Clout, M.Kretschmar, R.Jaenicke, C.Slingsby.

ABSTRACT

BACKGROUND: The betagamma-crystallins belong to a superfamily of two-domain proteins found in vertebrate eye lenses, with distant relatives occurring in microorganisms. It has been considered that an eukaryotic stress protein, spherulin 3a, from the slime mold Physarum polycephalum shares a common one-domain ancestor with crystallins, similar to the one-domain 3-D structure determined by NMR. RESULTS: The X-ray structure of spherulin 3a shows it to be a tight homodimer, which is consistent with ultracentrifugation studies. The (two-motif) domain fold contains a pair of calcium binding sites very similar to those found in a two-domain prokaryotic betagamma-crystallin fold family member, Protein S. Domain pairing in the spherulin 3a dimer is two-fold symmetric, but quite different in character from the pseudo-two-fold pairing of domains in betagamma-crystallins. There is no evidence that the spherulin 3a single domain can fold independently of its partner domain, a feature that may be related to the absence of a tyrosine corner. CONCLUSION: Although it is accepted that the vertebrate two-domain betagamma-crystallins evolved from a common one-domain ancestor, the mycetezoan single-domain spherulin 3a, with its unique mode of domain pairing, is likely to be an evolutionary offshoot, perhaps from as far back as the one-motif ancestral stage. The spherulin 3a protomer stability appears to be dependent on domain pairing. Spherulin-like domain sequences that are found within bacterial proteins associated with virulence are likely to bind calcium.

Selected figure(s)

Figure 6.
Figure 6. The Extensive Hydrophobic Interface Between Domains of the Spherulin s3a HomodimerThe appended side chains are listed in Table 1

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 115-124) copyright 2001.

Figure was selected by an automated process.