SASDDJ2: Calcium-bound polcalcin Phl p 7 (polcalcin Phl p 7)

Basic information

• Entry: Database: SASBDB / ID: SASDDJ2

Sample

Calcium-bound polcalcin Phl p 7

• polcalcin Phl p 7 (protein), Phleum pratense

• Function / homology: EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / calcium ion binding / Polcalcin Phl p 7
• Biological species: Phleum pratense (timothy grass)
• Citation: Journal: Proteins / Year: 2013; Title: Solution structures of polcalcin Phl p 7 in three ligation states: Apo-, hemi-Mg2+-bound, and fully Ca2+-bound.; Authors: Michael T Henzl / Arthur G Sirianni / Wei G Wycoff / Anmin Tan / John J Tanner / ; Abstract: Polcalcins are small EF-hand proteins believed to assist in regulating pollen-tube growth. Phl p 7, from timothy grass (Phleum pratense), crystallizes as a domain-swapped dimer at low pH. This study describes the solution structures of the recombinant protein in buffered saline at pH 6.0, containing either 5.0 mM EDTA, 5.0 mM Mg(2+), or 100 μM Ca(2+). Phl p 7 is monomeric in all three ligation states. In the apo-form, both EF-hand motifs reside in the closed conformation, with roughly antiparallel N- and C-terminal helical segments. In 5.0 mM Mg(2+), the divalent ion is bound by EF-hand 2, perturbing interhelical angles and imposing more regular helical structure. The structure of Ca(2+)-bound Phl p 7 resembles that previously reported for Bet v 4-likewise exposing apolar surface to the solvent. Occluded in the apo- and Mg(2+)-bound forms, this surface presumably provides the docking site for Phl p 7 targets. Unlike Bet v 4, EF-hand 2 in Phl p 7 includes five potential anionic ligands, due to replacement of the consensus serine residue at -x (residue 55 in Phl p 7) with aspartate. In the Phl p 7 crystal structure, D55 functions as a helix cap for helix D. In solution, however, D55 apparently serves as a ligand to the bound Ca(2+). When Mg(2+) resides in site 2, the D55 carboxylate withdraws to a distance consistent with a role as an outer-sphere ligand. (15)N relaxation data, collected at 600 MHz, indicate that backbone mobility is limited in all three ligation states.

Contact author

• John Tanner (Mizzou, University of Missouri-Columbia, Columbia, MO, USA)

Models

• Model #1715: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 3.74441090663; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Calcium-bound polcalcin Phl p 7 / Specimen concentration: 5.00-15.00
• Buffer: Name: 0.15M NaCl, 0.025M Hepes, pH 7.4, 100 uM Ca2+ / pH: 7.4

Entity #929

Type: protein / Description: polcalcin Phl p 7 / Formula weight: 8.545 / Num. of mol.: 1 / Source: Phleum pratense / References: UniProt: O82040
Sequence:

ADDMERIFKR FDTNGDGKIS LSELTDALRT LGSTSADEVQ RMMAEIDTDG DGFIDFNEFI SFCNANPGLM KDVAKVF

Experimental information

• Beam: Instrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS); City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1127 Å
• Detector: Name: MAR 165 CCD

Scan

Title: Calcium-bound Phl p 7 / Measurement date: Dec 8, 2011 / Cell temperature: 10 °C / Unit: 1/A /

	Min	Max
Q	0.021	0.3256

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 502 /

	Min	Max
Q	0.020978	0.325586
P(R) point	1	502
R	0	36.19

Result

Type of curve: single_conc /

	Experimental	Porod
MW	8.545 kDa	8.5 kDa
Volume	-	13.6 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	52.19	52.54	0.075
Radius of gyration, Rg	1.27 nm	1.29 nm	0.003

	Min	Max
D	-	3.62
Guinier point	1	132