Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 44.70 kDa 
• Atom Count: 2758 
• Modelled Residue Count: 363 
• Deposited Residue Count: 424 
• Unique protein chains: 1

2NMR

An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance

• PDB DOI: 10.2210/pdb2NMR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2006-10-23 Released: 2006-11-14 
• Deposition Author(s): Lupo, D., Winkler, F.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance

Javelle, A., Lupo, D., Zheng, L., Li, X.-D., Winkler, F.K., Merrick, M.

(2006) J Biol Chem 281: 39492-39498

• PubMed: 17040913 
• DOI: 10.1074/jbc.M608325200
• Primary Citation of Related Structures:  
  2NMR, 2NOP, 2NOW, 2NPC, 2NPD, 2NPE, 2NPG, 2NPJ, 2NPK


• PubMed Abstract: 
  

Amt proteins constitute a class of ubiquitous integral membrane proteins that mediate movement of ammonium across cell membranes. They are homotrimers, in which each subunit contains a narrow pore through which substrate transport occurs. Two conserved histidine residues in the pore have been proposed to be necessary for ammonia conductance. By analyzing 14 engineered polar and non-polar variants of these histidines, in Escherichia coli AmtB, we show that both histidines are absolutely required for optimum substrate conductance. Crystal structures of variants confirm that substitution of the histidine residues does not affect AmtB structure. In a subgroup of Amt proteins, found only in fungi, one of the histidines is replaced by glutamate. The equivalent substitution in E. coli AmtB is partially active, and the structure of this variant suggests that the glutamate side chain can make similar interactions to those made by histidine.

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Organizational Affiliation: 

Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, Norfolk, NR4 7UH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonia channel	A	424	Escherichia coli	Mutation(s): 0  Gene Names: amtB Membrane Entity: Yes
UniProt
Find proteins for P69681 (Escherichia coli (strain K12)) Explore P69681  Go to UniProtKB:  P69681

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.195 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.799	α = 90
b = 109.799	β = 90
c = 84.407	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-23 
• Released Date: 2006-11-14 
Deposition Author(s): Lupo, D., Winkler, F.K.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description