PDBsum entry 1s3p

Calcium-binding protein

PDB id: 1s3p

Contents

Protein chain

109 a.a. *

Ligands

SO4

Metals

_CA ×2

Waters ×129

* Residue conservation analysis

PDB id:

1s3p

Name:

Calcium-binding protein

Title:

Crystal structure of rat alpha-parvalbumin s55d/e59d mutant

Structure:

Parvalbumin alpha. Chain: a. Engineered: yes. Mutation: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: pvalb, pva. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.181 R-free: 0.221

Authors:

J.J.Tanner,M.T.Henzl

Key ref:

Y.H.Lee et al. (2004). Crystal structure of a high-affinity variant of rat alpha-parvalbumin. Biochemistry, 43, 10008-10017. PubMed id: 15287728 DOI: 10.1021/bi0492915

Date:

13-Jan-04 Release date: 07-Sep-04

Protein chain

P02625  (PRVA_RAT) -  Parvalbumin alpha from Rattus norvegicus

Seq: 110 a.a.

Struc: 109 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/bi0492915

Biochemistry 43:10008-10017 (2004)

PubMed id: 15287728

Crystal structure of a high-affinity variant of rat alpha-parvalbumin.

Y.H.Lee, J.J.Tanner, J.D.Larson, M.T.Henzl.

ABSTRACT

In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs containing four carboxylates positioned on the +x and -x and +z and -z axes; introduction of a fifth carboxylate ligand reduces the affinity. However, in rat beta-parvalbumin, replacement of Ser-55 with aspartate heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry 35, 5856-5869]. The corresponding alpha-parvalbumin variant (S55D/E59D) likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal. Biochem. 319, 216-233]. To determine whether these mutations produce a variation on the archetypal EF-hand coordination scheme, we have obtained high-resolution X-ray crystallographic data for alpha S55D/E59D. As anticipated, the aspartyl carboxylate replaces the serine hydroxyl at the +z coordination position. Interestingly, the Asp-59 carboxylate abandons the role it plays as an outer sphere ligand in wild-type rat beta, rotating away from the Ca2+ and, instead, forming a hydrogen bond with the amide of Glu-62. Superficially, the coordination sphere in the CD site of alpha S55D/E59D resembles that in the EF site. However, the orientation of the Asp-59 side chain is predicted to stabilize the D-helix, which may contribute to the heightened divalent ion affinity. DSC data indicate that the alpha S55D/E59D variant retains the capacity to bind 1 equiv of Na+. Consistent with this finding, when binding measurements are conducted in K(+)-containing buffer, divalent ion affinity is markedly higher. In 0.15 M KCl and 0.025 M Hepes-KOH (pH 7.4) at 5 degrees C, the macroscopic Ca2+ binding constants are 1.8 x 10(10) and 2.0 x 10(9) M(-1). The corresponding Mg2+ binding constants are 2.7 x 10(6) and 1.2 x 10(5) M(-1).