PDBsum entry: 2ns1

Transport protein/signaling protein

PDB id: 2ns1

Contents

Protein chains

404 a.a. *

113 a.a. *

Ligands

BOG ×8

TRS ×2

ADP

Waters ×498

* Residue conservation analysis

PDB id:

2ns1

Name:

Transport protein/signaling protein

Title:

Crystal structure of the e. Coli ammonia channel amtb comple the signal transduction protein glnk

Structure:

Ammonia channel. Chain: a. Fragment: residues 23-428. Synonym: ammonia transporter. Engineered: yes. Nitrogen regulatory protein p-ii 2. Chain: b. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: amtb. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: glnk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.96Å R-factor: 0.164 R-free: 0.198

Authors:

F.Gruswitz,J.O'Connell Iii,R.M.Stroud,Center For Structures Membrane Proteins (Csmp)

Key ref:

F.Gruswitz et al. (2007). Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. Proc Natl Acad Sci U S A, 104, 42-47. PubMed id: 17190799 DOI: 10.1073/pnas.0609796104

Date:

02-Nov-06 Release date: 26-Dec-06

Protein chain

P69681  (AMTB_ECOLI) -  Ammonia channel

Seq: 428 a.a.

Struc: 404 a.a.

Protein chain

P0AC55  (GLNK_ECOLI) -  Nitrogen regulatory protein P-II 2

Seq: 112 a.a.

Struc: 113 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (3 terms)
• Biological process: ammonium transmembrane transport (8 terms)
• Biochemical function: enzyme regulator activity (6 terms)

DOI no: 10.1073/pnas.0609796104

Proc Natl Acad Sci U S A 104:42-47 (2007)

PubMed id: 17190799

Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A.

F.Gruswitz, J.O'Connell, R.M.Stroud.

ABSTRACT

Ammonia conductance is highly regulated. A P(II) signal transduction protein, GlnK, is the final regulator of transmembrane ammonia conductance by the ammonia channel AmtB in Escherichia coli. The complex formed between AmtB and inhibitory GlnK at 1.96-A resolution shows that the trimeric channel is blocked directly by GlnK and how, in response to intracellular nitrogen status, the ability of GlnK to block the channel is regulated by uridylylation/deuridylylation at Y51. ATP and Mg(2+) augment the interaction of GlnK. The hydrolyzed product, adenosine 5'-diphosphate orients the surface of GlnK for AmtB blockade. 2-Oxoglutarate diminishes AmtB/GlnK association, and sites for 2-oxoglutarate are evaluated.

Selected figure(s)

Figure 2.
Fig. 2. Monomer to monomer AmtB/Glnk interaction and comparison to uncomplexed structures. (A) Stereoview of a single inhibitory interaction (one asymmetric unit) between GlnK and AmtB. A ribbon diagram of AmtB (blue) and GlnK (red) is oriented identically to the matching colored monomers in Fig. 1. ADP bound to GlnK is shown in stick representation. (B) An overlay of the backbone of AmtB (blue) and GlnK (red) in the complex, compared with structures of the uncomplexed proteins [AmtB, 1U7G (black) and Amt1, 2B2H (green)]. Two loops of AmtB on the cytoplasmic side in the shaded region i are arranged differently from uncomplexed AmtB, with corresponding differences in 21 residues at the C terminus (dashed region ii). The complexed form of the AmtB C terminus is the same as that in uncomplexed Amt1. The T-loop of GlnK becomes highly ordered in the ADP-bound inhibitory complex vs. disordered in uncomplexed ATP-bound GlnK [2GNK (orange), dotted region iii].

Figure 3.
Fig. 3. Channel inhibition and ammonia conductance pathway. Blockade of the ammonia conduction pathway by R47 of GlnK (red) is in context (Center) and in detail (Left). The surface of AmtB (blue) is shown with residues 211–270 as a tubular backbone trace to reveal the hydrophobic channel behind (Right). Side chains of residues in AmtB along the conduction pathway (F107, F215,H168, and H318) and residues that interact with R47 (S263, D313, and carbonyl of C312) are in ball-and-stick representation with nitrogen (dark blue) and oxygen (light red) shown. The location of L259 (blue sphere on the tubular trace) and V299 that forms part of the surface is indicated. Ammonia positions (Am2, Am3, and Am4) seen only in uncomplexed AmtB are indicated as yellow spheres. In the complex, there are only two water/NH[3] sites within the channel (Am6 and Am5). Waters within 6 Å of the channel and hydrophobic portals are shown as green spheres. A molecule of Tris (a quaternary ammonium cation, C+) displaced NH at the periplasmic "recruitment site" (top right).

Figures were selected by an automated process.