PDBsum entry 1g9x

Structural genomics

PDB id: 1g9x

Contents

Protein chains

253 a.a. *

Ligands

MMC ×3

ADP ×3

Metals

_MG ×3

Waters ×143

* Residue conservation analysis

PDB id:

1g9x

Name:

Structural genomics

Title:

Characterization of the twinning structure of mj1267, an atp-binding cassette of an abc transporter

Structure:

High-affinity branched-chain amino acid transport atp- binding protein. Chain: a, b, c. Fragment: mj1267. Engineered: yes. Mutation: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: structural DNA. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.60Å R-factor: 0.153 R-free: 0.279

Authors:

Y.-R.Yuan,J.F.Hunt

Key ref:

Y.R.Yuan et al. (2003). Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packing. Acta Crystallogr D Biol Crystallogr, 59, 225-238. PubMed id: 12554933 DOI: 10.1107/S0907444902018954

Date:

28-Nov-00 Release date: 11-Feb-03

Protein chains

Q58663  (LIVG_METJA) -  Probable branched-chain amino acid transport ATP-binding protein LivG from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 257 a.a.

Struc: 253 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1107/S0907444902018954

Acta Crystallogr D Biol Crystallogr 59:225-238 (2003)

PubMed id: 12554933

Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packing.

Y.R.Yuan, O.Martsinkevich, J.F.Hunt.

ABSTRACT

ATP-binding cassettes represent the motor domains in ABC transporters, a superfamily of integral membrane-protein pumps that couple the hydrolysis of ATP to transmembrane solute translocation. A crystal of a Mg-ADP complex of the MJ1267 ATP-binding cassette was obtained that produced a diffraction pattern characterized by pathological streaking of the spots in the a* x b* plane. While the Laue symmetry of the diffraction pattern was P3;1m, the crystal was determined to be twinned based on intensity statistics, molecular-replacement analysis and difference Fourier analysis of an engineered single-site methylmercury derivative. The unit cell contains three similar 3(1) fibers, with two of them related by primarily translational non-crystallographic symmetry (NCS) and the third related to the first two by approximate twofold screw operations whose rotational components are very similar to the twinning operator. The promiscuous packing of these 3(1) fibers, which make both parallel and antiparallel interactions in the primary crystal lattice, can explain the twinning tendency based on the ability of the twin-related lattices to interact with one another while making only one slightly sub-optimal intermolecular contact per unit cell in the boundary region. The promiscuous fiber packing can also explain the streaking in the diffraction pattern based on the ability to form a variety of different lattices with similar inter-fiber packing interactions. The crystal structure was refined as a twin in space group P3(1) using the program CNS, yielding a free R factor of 28.9% at 2.6 A and a refined twin fraction of 0.50. The structure shows a rigid-body rotation of the ABC-transporter-specific alpha-helical subdomain (ABCalpha subdomain) in MJ1267 compared with the conformation observed for the same protein in a C2 crystal lattice; this observation suggests that the ABCalpha subdomain is flexibly attached to the F1-type ATP-binding core of the ATP-binding cassette when Mg-ADP is bound at the active site.

Selected figure(s)

Figure 1.
Figure 1 The trigonal crystal form of MJ1267. (a) Photomicrograph of typical crystals in approximately 18%(w/v) PEG 3350, 15%(v/v) ethylene glycol, 10%(v/v) glycerol, 0.1 mM DTT, 10 mM Mg-ADP, 100 mM MES pH 5.9. (b) A 1° oscillation frame from a selenomethionine-labeled crystal of the wild-type protein collected at 12 900 eV on beamline X4A at the NSLS (displayed with the program XDISP; Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.]). (c) A magnified view of the region of the diffraction image in (a) delineated by the black square.

Figure 5.
Figure 5 Stereo pairs showing refined structures of the Mg-ADP-bound MJ1267 protein. The molecules are color-coded according to domain organization (Karpowich et al., 2001[Karpowich, N., Martsinkevich, O., Millen, L., Yuan, Y.-R., Dai, P. L., MacVey, K., Thomas, P. J. & Hunt, J. F. (2001). Structure, 9, 571-586.]), with green showing the antiparallel -sheet subdomain (ABC ), red showing the F1-type ATP-binding core, blue showing the -helical subdomain (ABC ) and magenta showing the -phosphate linker which connects the ABC subdomain to the ATP-binding core. The images were produced using MOLSCRIPT and RASTER3D (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]; Merritt & Bacon, 1997[Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.]). (a) Comparison of the structure of one of the NCS-related molecules in the twinned trigonal crystal (darker colors) with the structure of the same protein in the untwinned monoclinic crystal obtained from the methylmercury derivative of the N109C mutant of MJ1267 (lighter colors) (Karpowich et al., 2001[Karpowich, N., Martsinkevich, O., Millen, L., Yuan, Y.-R., Dai, P. L., MacVey, K., Thomas, P. J. & Hunt, J. F. (2001). Structure, 9, 571-586.]). The protein has Mg-ADP bound at the active site in both crystal structures. The molecules were aligned based on least-squares superposition of the -strands and P-loop helix from the F1-type ATP-binding core. Subunit A (the `1+' molecule) is shown from the twinned trigonal crystal structure. (b) Comparison of the three refined NCS-related molecules in the asymmetric unit of the twinned trigonal crystal after least-squares superposition of the the -strands and P-loop helix from the F1-type ATP-binding core. (c) Comparison of the three refined NCS-related molecules in the asymmetric unit of the twinned trigonal crystal after least-squares superposition of the -helices in the ABC subdomain.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 225-238) copyright 2003.

Figures were selected by an automated process.