PDBsum entry 2k3m

Membrane protein

PDB id

2k3m

Contents

			Protein chain

					127 a.a.

			Ligands

					MTN ×3

References listed in PDB file

Key reference

Title

Backbone structure of a small helical integral membrane protein: a unique structural characterization.

Authors

R.C.Page, S.Lee, J.D.Moore, S.J.Opella, T.A.Cross.

Ref.

Protein Sci, 2009, 18, 134-146. [DOI no: 10.1002/pro.24]

PubMed id

19177358

Abstract

The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three-dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C-terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 A rmsd backbone structure with a transmembrane domain defined at 0.40 A. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long-range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins.



	Figure 3. The 30 lowest energy backbone structures (A) are shown in a wide-eyed stereo diagram along with a ribbon diagram of the lowest energy structure (B). The ribbon representation clearly shows the kink of the TM helix and helical propensity of the EM domain. Both diagrams are colored from blue (amino terminus) to red (carboxyl terminus). Structures are aligned to the average backbone structure using all N[H], C[[alpha]], and C[prime prime or minute] atoms.		Figure 5. The EM domain of Rv1761c is characterized by a set of four helices (A, B). These four helices are organized such that H4 and H5 are co-planar and both H3 and H6 are behind the H4/H5 plane (A, B). The helical domain is shown as a ribbon model (A) and a backbone trace for the 30 lowest energy structures (B) colored in a rainbow (as in Fig. 3A Figure 3-, B). The 30 superimposed backbone structures (B) are aligned to the average backbone structure using N[H], C[[alpha]], and C[prime prime or minute] atoms from helices H3, H4, H5, and H6 (Residues 59 --67, 73 --86, 90 --103, and 110 --120). The U-shaped H4/H5 helical pair forms a hydrophobic surface (C) with the amphipathic Helix H6 situated just below the H4/H5 plane and the hydrophilic Helix H3 located well below the H4/H5 plane (D). For C, D positively charged residues are colored red (Arg, His, Lys), negatively charged residues are colored blue (Asp, Glu), nonpolar residues are colored grey (Ala, Gly, Ile, Leu, Met, Pro, Phe, Ser, Thr, Val) and polar uncharged residues are colored green (Asn, Cys, Gln, Trp, Tyr). Throughout this figure, the flexible carboxyl terminal region (residues 122 --127) and the flexible linker region between the TM and H3 are not shown. Arrows and axes indicate the approximate rotations used to transform between the orientations depicted in A, C, and D. Figure generated using PyMOL.44.

PROCHECK

	Headers