PDBsum entry 2b2f

Transport protein

PDB id: 2b2f

Contents

Protein chain

391 a.a. *

Waters ×149

* Residue conservation analysis

PDB id:

2b2f

Name:

Transport protein

Title:

Ammonium transporter amt-1 from a.Fulgidus (native)

Structure:

Ammonium transporter. Chain: a. Synonym: amt-1. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: amt1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.72Å R-factor: 0.181 R-free: 0.200

Authors:

S.L.Andrade,A.Dickmanns,R.Ficner,O.Einsle

Key ref:

S.L.Andrade et al. (2005). Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc Natl Acad Sci U S A, 102, 14994-14999. PubMed id: 16214888 DOI: 10.1073/pnas.0506254102

Date:

19-Sep-05 Release date: 11-Oct-05

Protein chain

O29285  (O29285_ARCFU) -  Ammonium transporter Amt1 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 391 a.a.

Struc: 391 a.a.

DOI no: 10.1073/pnas.0506254102

Proc Natl Acad Sci U S A 102:14994-14999 (2005)

PubMed id: 16214888

Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus.

S.L.Andrade, A.Dickmanns, R.Ficner, O.Einsle.

ABSTRACT

Ammonium transporters (Amts) are integral membrane proteins found in all kingdoms of life that fulfill an essential function in the uptake of reduced nitrogen for biosynthetic purposes. Amt-1 is one of three Amts encoded in the genome of the hyperthermophilic archaeon Archaeoglobus fulgidus. The crystal structure of Amt-1 shows a compact trimer with 11 transmembrane helices per monomer and a central channel for substrate conduction in each monomer, similar to the known crystal structure of AmtB from Escherichia coli. Xenon derivatization has been used to identify apolar regions of Amt-1, emphasizing not only the hydrophobicity of the substrate channel but also the unexpected presence of extensive internal cavities that should be detrimental for protein stability. The substrates ammonium and methylammonium have been used for cocrystallization experiments with Amt-1, but the identification of binding sites that are distinct from water positions is not unambiguous. The well ordered cytoplasmic C terminus of the protein in the Amt-1 structure has allowed for the construction of a docking model between Amt-1 and a homology model for its physiological interaction partner, the P(II) protein GlnB-1. In this model, GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively blocking conduction through the three individual substrate channels.

Selected figure(s)

Figure 2.
Fig. 2. Structure of A. fulgidus Amt-1. (A) Stereo representation of the Amt-1 monomer. The membrane is indicated in gray, with the extracellular side above and the cytoplasmic side below. The protein chain is colored from blue at the N terminus to red at the C terminus, the 11 transmembrane helices numbered in accordance with Fig. 1. (B) The Amt-1 trimer seen from the extracellular side. (C) B factor representation of Amt-1. The region with the highest B factors is in the loop between helices V and VI, connecting the pseudosymmetry-related halves of the protein.

Figure 4.
Fig. 4. Ammonium recruitment site and substrate channel. presumably forms a hydrogen bond to the side chain of S208 on the extracellular side of Amt-1 (at the top), stabilized by a interaction with the side chain of W137. The hydrophobic channel leading to the cytoplasmic side is blocked by F96 and F204, with the latter having significantly elevated B factors, an indication of structural flexibility. The N[ ]atoms of two conserved histidine residues, H157 and H305, are in hydrogen-bonding distance and their imidazole rings are almost perfectly coplanar.

Figures were selected by an automated process.