PDBsum entry 1vfp

Hydrolase

PDB id: 1vfp

Contents

Protein chains

994 a.a. *

Ligands

ACP ×2

Metals

_CA ×4

_MG ×2

Waters ×8

* Residue conservation analysis

PDB id:

1vfp

Name:

Hydrolase

Title:

Crystal structure of the sr ca2+-atpase with bound amppcp

Structure:

Sarcoplasmic/endoplasmic reticulum calcium atpase 1. Chain: a, b. Synonym: ca2+-atpase, serca1. Ec: 3.6.3.8

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: skeletal muscle (white)

Resolution:

2.90Å R-factor: 0.247 R-free: 0.287

Authors:

C.Toyoshima,T.Mizutani

Key ref:

C.Toyoshima and T.Mizutani (2004). Crystal structure of the calcium pump with a bound ATP analogue. Nature, 430, 529-535. PubMed id: 15229613 DOI: 10.1038/nature02680

Date:

18-Apr-04 Release date: 06-Jul-04

Protein chains

P04191  (AT2A1_RABIT) -  Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 from Oryctolagus cuniculus

Seq: 1001 a.a.

Struc: 994 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.7.2.2.10 - P-type Ca(2+) transporter.
• Reaction: Ca²⁺(in) + ATP + H2O = Ca²⁺(out) + ADP + phosphate + H⁺

Ca(2+)(in) + ATP + H2O = Ca(2+)(out) (Bound ligand (Het Group name = ACP) matches with 81.25% similarity) + ADP + phosphate + H(+)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature02680

Nature 430:529-535 (2004)

PubMed id: 15229613

Crystal structure of the calcium pump with a bound ATP analogue.

C.Toyoshima, T.Mizutani.

ABSTRACT

P-type ATPases are ATP-powered ion pumps that establish ion concentration gradients across cell and organelle membranes. Here, we describe the crystal structure of the Ca2+ pump of skeletal muscle sarcoplasmic reticulum, a representative member of the P-type ATPase superfamily, with an ATP analogue, a Mg2+ and two Ca2+ ions in the respective binding sites. In this state, the ATP analogue reorganizes the three cytoplasmic domains (A, N and P), which are widely separated without nucleotide, by directly bridging the N and P domains. The structure of the P-domain itself is altered by the binding of the ATP analogue and Mg2+. As a result, the A-domain is tilted so that one of the transmembrane helices moves to lock the cytoplasmic gate of the transmembrane Ca2+-binding sites. This appears to be the mechanism for occluding the bound Ca2+ ions, before releasing them into the lumen of the sarcoplasmic reticulum.

Selected figure(s)

Figure 3.
Figure 3: Transmembrane Ca^2+-binding sites (I and II) and the movement of the M1 helix.
a, E1 2Ca^2+; b, E1 AMPPCP; c, superimposition of E1 2Ca^2+ (violet) and E1 AMPPCP (atom colour) in stereo view. Cyan (a–c) and violet spheres (c) represent bound Ca^2+; red spheres indicate water molecules in the crystals. Owing to the resolution limitation of the diffraction data, no water molecules are shown in b. Dotted lines in c show the coordination of Ca^2+ and hydrogen bonds involving E309 and D800 side chains.

Figure 4.
Figure 4: Omit-annealed F[o] - F[c] map around AMPPCP at 5 sigma-(a) and the hydrogen-bonding network around AMPPCP (b). AMPPCP is shown in ball-and-stick representation; the N- and P-domains are coloured light green and orange, respectively. Light-green broken lines in b show likely hydrogen bonds. A part of the N-domain is removed for clarity. Small spheres represent Mg^2+ (green) and two water molecules (red), which coordinate to the Mg^2+, together with -phosphate, carboxyl groups of Asp 351 and Asp703, and a carbonyl group of Thr 353 (orange broken lines in a and dark-green lines in b).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 430, 529-535) copyright 2004.

Figures were selected by an automated process.