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PDBsum entry 1xqe

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Transport protein PDB id
1xqe
Jmol
Contents
Protein chain
366 a.a. *
Ligands
SO4 ×3
ACT
Waters ×93
* Residue conservation analysis
PDB id:
1xqe
Name: Transport protein
Title: The mechanism of ammonia transport based on the crystal stru amtb of e. Coli.
Structure: Probable ammonium transporter. Chain: a. Synonym: ammonia transporter. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.10Å     R-factor:   0.161     R-free:   0.186
Authors: L.Zheng,D.Kostrewa,S.Berneche,F.K.Winkler,X.-D.Li
Key ref:
L.Zheng et al. (2004). The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proc Natl Acad Sci U S A, 101, 17090-17095. PubMed id: 15563598 DOI: 10.1073/pnas.0406475101
Date:
12-Oct-04     Release date:   26-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P69681  (AMTB_ECOLI) -  Ammonia channel
Seq:
Struc:
428 a.a.
366 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     ammonium transmembrane transport   4 terms 
  Biochemical function     uniporter activity     2 terms  

 

 
DOI no: 10.1073/pnas.0406475101 Proc Natl Acad Sci U S A 101:17090-17095 (2004)
PubMed id: 15563598  
 
 
The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli.
L.Zheng, D.Kostrewa, S.Bernèche, F.K.Winkler, X.D.Li.
 
  ABSTRACT  
 
Ammonium is one of the most important nitrogen sources for bacteria, fungi, and plants, but it is toxic to animals. The ammonium transport proteins (methylamine permeases/ammonium transporters/rhesus) are present in all domains of life; however, functional studies with members of this family have yielded controversial results with respect to the chemical identity (NH(4)(+) or NH(3)) of the transported species. We have solved the structure of wild-type AmtB from Escherichia coli in two crystal forms at 1.8- and 2.1-A resolution, respectively. Substrate transport occurs through a narrow mainly hydrophobic pore located at the center of each monomer of the trimeric AmtB. At the periplasmic entry, a binding site for NH(4)(+) is observed. Two phenylalanine side chains (F107 and F215) block access into the pore from the periplasmic side. Further into the pore, the side chains of two highly conserved histidine residues (H168 and H318) bridged by a H-bond lie adjacent, with their edges pointing into the cavity. These histidine residues may facilitate the deprotonation of an ammonium ion entering the pore. Adiabatic free energy calculations support the hypothesis that an electrostatic barrier between H168 and H318 hinders the permeation of cations but not that of the uncharged NH(3.) The structural data and energetic considerations strongly indicate that the methylamine permeases/ammonium transporters/rhesus proteins are ammonia gas channels. Interestingly, at the cytoplasmic exit of the pore, two different conformational states are observed that might be related to the inactivation mechanism by its regulatory partner.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Topological representation of the AmtB monomer. (a) Side view from the membrane. (b) Top view from the extracellular side.
Figure 5.
Fig. 5. Conformational change at the cytoplasmic exit between R3 and P6[3] crystal structures. The pore is viewed from the cytoplasmic side. (a) R3 structure ("open" exit conformation). (b)P6[3] structure ("closed" exit conformation).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20927037 C.A.Wagner, O.Devuyst, H.Belge, S.Bourgeois, and P.Houillier (2011).
The rhesus protein RhCG: a new perspective in ammonium transport and distal urinary acidification.
  Kidney Int, 79, 154-161.  
21127027 L.Graff, P.Obrdlik, L.Yuan, D.Loqué, W.B.Frommer, and N.von Wirén (2011).
N-terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1.
  J Exp Bot, 62, 1361-1373.  
21283535 L.Wang, L.Lai, Q.Ouyang, and C.Tang (2011).
Flux Balance Analysis of Ammonia Assimilation Network in E. coli Predicts Preferred Regulation Point.
  PLoS One, 6, e16362.  
21368153 U.Akgun, and S.Khademi (2011).
Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily.
  Proc Natl Acad Sci U S A, 108, 3970-3975.  
21220112 Y.Sonoda, S.Newstead, N.J.Hu, Y.Alguel, E.Nji, K.Beis, S.Yashiro, C.Lee, J.Leung, A.D.Cameron, B.Byrne, S.Iwata, and D.Drew (2011).
Benchmarking membrane protein detergent stability for improving throughput of high-resolution X-ray structures.
  Structure, 19, 17-25.  
20010838 A.B.Waight, J.Love, and D.N.Wang (2010).
Structure and mechanism of a pentameric formate channel.
  Nat Struct Mol Biol, 17, 31-37.
PDB codes: 3kly 3klz
19953292 C.H.Huang, and M.Ye (2010).
The Rh protein family: gene evolution, membrane biology, and disease association.
  Cell Mol Life Sci, 67, 1203-1218.  
20457942 F.Gruswitz, S.Chaudhary, J.D.Ho, A.Schlessinger, B.Pezeshki, C.M.Ho, A.Sali, C.M.Westhoff, and R.M.Stroud (2010).
Function of human Rh based on structure of RhCG at 2.1 A.
  Proc Natl Acad Sci U S A, 107, 9638-9643.
PDB code: 3hd6
20126667 I.Mouro-Chanteloup, S.Cochet, M.Chami, S.Genetet, N.Zidi-Yahiaoui, A.Engel, Y.Colin, O.Bertrand, and P.Ripoche (2010).
Functional reconstitution into liposomes of purified human RhCG ammonia channel.
  PLoS One, 5, e8921.  
21048711 J.L.Robertson, L.Kolmakova-Partensky, and C.Miller (2010).
Design, function and structure of a monomeric ClC transporter.
  Nature, 468, 844-847.
PDB code: 3nmo
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
  21048002 O.K.Kamneva, D.A.Liberles, and N.L.Ward (2010).
Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.
  Genome Biol Evol, 2, 870-886.  
19581303 D.Loqué, S.I.Mora, S.L.Andrade, O.Pantoja, and W.B.Frommer (2009).
Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity.
  J Biol Chem, 284, 24988-24995.  
19865084 E.J.Levin, M.Quick, and M.Zhou (2009).
Crystal structure of a bacterial homologue of the kidney urea transporter.
  Nature, 462, 757-761.
PDB codes: 3k3f 3k3g
19015848 H.Wang, F.Wang, and D.Wei (2009).
Impact of oxygen supply on rtPA expression in Escherichia coli BL21 (DE3): ammonia effects.
  Appl Microbiol Biotechnol, 82, 249-259.  
  21468180 K.H.Han, H.Y.Kim, and I.D.Weiner (2009).
Expression of rh glycoproteins in the Mammalian kidney.
  Electrolyte Blood Press, 7, 14-19.  
18931342 L.J.Bruce, H.Guizouarn, N.M.Burton, N.Gabillat, J.Poole, J.F.Flatt, R.L.Brady, F.Borgese, J.Delaunay, and G.W.Stewart (2009).
The monovalent cation leak in overhydrated stomatocytic red blood cells results from amino acid substitutions in the Rh-associated glycoprotein.
  Blood, 113, 1350-1357.  
19073648 L.Yuan, L.Graff, D.Loqué, S.Kojima, Y.N.Tsuchiya, H.Takahashi, and N.von Wirén (2009).
AtAMT1;4, a Pollen-Specific High-Affinity Ammonium Transporter of the Plasma Membrane in Arabidopsis.
  Plant Cell Physiol, 50, 13-25.  
19609355 M.Pellegrini-Calace, T.Maiwald, and J.M.Thornton (2009).
PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
  PLoS Comput Biol, 5, e1000440.  
19007411 P.L.Tremblay, and P.C.Hallenbeck (2009).
Of blood, brains and bacteria, the Amt/Rh transporter family: emerging role of Amt as a unique microbial sensor.
  Mol Microbiol, 71, 12-22.  
19242745 R.Musa-Aziz, L.Jiang, L.M.Chen, K.L.Behar, and W.F.Boron (2009).
Concentration-dependent effects on intracellular and surface pH of exposing Xenopus oocytes to solutions containing NH3/NH4(+).
  J Membr Biol, 228, 15-31.  
19273840 R.Musa-Aziz, L.M.Chen, M.F.Pelletier, and W.F.Boron (2009).
Relative CO2/NH3 selectivities of AQP1, AQP4, AQP5, AmtB, and RhAG.
  Proc Natl Acad Sci U S A, 106, 5406-5411.  
19340454 R.Søgaard, M.Alsterfjord, N.Macaulay, and T.Zeuthen (2009).
Ammonium ion transport by the AMT/Rh homolog TaAMT1;1 is stimulated by acidic pH.
  Pflugers Arch, 458, 733-743.  
19884311 W.B.Inwood, J.A.Hall, K.S.Kim, R.Fong, and S.Kustu (2009).
Genetic evidence for an essential oscillation of transmembrane-spanning segment 5 in the Escherichia coli ammonium channel AmtB.
  Genetics, 183, 1341-1355.  
19278252 Y.Lin, Z.Cao, and Y.Mo (2009).
Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB.
  J Phys Chem B, 113, 4922-4929.  
18362341 A.Javelle, D.Lupo, P.Ripoche, T.Fulford, M.Merrick, and F.K.Winkler (2008).
Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.
  Proc Natl Acad Sci U S A, 105, 5040-5045.
PDB codes: 3c1g 3c1h 3c1i 3c1j
  18923187 B.Martinac, Y.Saimi, and C.Kung (2008).
Ion channels in microbes.
  Physiol Rev, 88, 1449-1490.  
18245289 B.Walter, M.Küspert, D.Ansorge, R.Krämer, and A.Burkovski (2008).
Dissection of ammonium uptake systems in Corynebacterium glutamicum: mechanism of action and energetics of AmtA and AmtB.
  J Bacteriol, 190, 2611-2614.  
  19825599 C.Yoshihara, K.Inoue, D.Schichnes, S.Ruzin, W.Inwood, and S.Kustu (2008).
An Rh1-GFP fusion protein is in the cytoplasmic membrane of a white mutant strain of Chlamydomonas reinhardtii.
  Mol Plant, 1, 1007-1020.  
18405331 J.A.Raven, M.Giordano, and J.Beardall (2008).
Insights into the evolution of CCMs from comparisons with other resource acquisition and assimilation processes.
  Physiol Plant, 133, 4.  
18434596 J.C.Rutherford, G.Chua, T.Hughes, M.E.Cardenas, and J.Heitman (2008).
A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae.
  Mol Biol Cell, 19, 3028-3039.  
18055915 J.C.Rutherford, X.Lin, K.Nielsen, and J.Heitman (2008).
Amt2 Permease Is Required To Induce Ammonium-Responsive Invasive Growth and Mating in Cryptococcus neoformans.
  Eukaryot Cell, 7, 237-246.  
19108721 J.H.Kirsten, Y.Xiong, C.T.Davis, and C.K.Singleton (2008).
Subcellular localization of ammonium transporters in Dictyostelium discoideum.
  BMC Cell Biol, 9, 71.  
18832935 N.M.Burton, and D.J.Anstee (2008).
Structure, function and significance of Rh proteins in red cells.
  Curr Opin Hematol, 15, 625-630.  
18156251 P.L.Tremblay, and P.C.Hallenbeck (2008).
Ammonia-induced formation of an AmtB-GlnK complex is not sufficient for nitrogenase regulation in the photosynthetic bacterium Rhodobacter capsulatus.
  J Bacteriol, 190, 1588-1594.  
17921289 B.Cherif-Zahar, A.Durand, I.Schmidt, N.Hamdaoui, I.Matic, M.Merrick, and G.Matassi (2007).
Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea.
  J Bacteriol, 189, 9090-9100.  
17198846 C.M.Westhoff (2007).
The structure and function of the Rh antigen complex.
  Semin Hematol, 44, 42-50.  
17291160 D.L.Bostick, and C.L.Brooks (2007).
Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.
  PLoS Comput Biol, 3, e22.  
17434945 D.L.Bostick, and C.L.Brooks (2007).
On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.
  Biophys J, 92, L103-L105.  
18032606 D.Lupo, X.D.Li, A.Durand, T.Tomizaki, B.Cherif-Zahar, G.Matassi, M.Merrick, and F.K.Winkler (2007).
The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins.
  Proc Natl Acad Sci U S A, 104, 19303-19308.
PDB code: 3b9w
17190799 F.Gruswitz, J.O'Connell, and R.M.Stroud (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.
PDB code: 2ns1
17490609 G.L.Lorca, R.D.Barabote, V.Zlotopolski, C.Tran, B.Winnen, R.N.Hvorup, A.J.Stonestrom, E.Nguyen, L.W.Huang, D.S.Kim, and M.H.Saier (2007).
Transport capabilities of eleven gram-positive bacteria: comparative genomic analyses.
  Biochim Biophys Acta, 1768, 1342-1366.  
17351012 G.Lamoureux, M.L.Klein, and S.Bernèche (2007).
A stable water chain in the hydrophobic pore of the AmtB ammonium transporter.
  Biophys J, 92, L82-L84.  
17098799 H.Yang, Y.Xu, W.Zhu, K.Chen, and H.Jiang (2007).
Detailed mechanism for AmtB conducting NH4+/NH3: molecular dynamics simulations.
  Biophys J, 92, 877-885.  
17002591 I.D.Weiner, and L.L.Hamm (2007).
Molecular mechanisms of renal ammonia transport.
  Annu Rev Physiol, 69, 317-340.  
17704220 J.Paz-Yepes, A.Herrero, and E.Flores (2007).
The NtcA-regulated amtB gene is necessary for full methylammonium uptake activity in the cyanobacterium Synechococcus elongatus.
  J Bacteriol, 189, 7791-7798.  
17493133 M.Boeckstaens, B.André, and A.M.Marini (2007).
The yeast ammonium transport protein Mep2 and its positive regulator, the Npr1 kinase, play an important role in normal and pseudohyphal growth on various nitrogen media through retrieval of excreted ammonium.
  Mol Microbiol, 64, 534-546.  
17220269 M.J.Conroy, A.Durand, D.Lupo, X.D.Li, P.A.Bullough, F.K.Winkler, and M.Merrick (2007).
The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel.
  Proc Natl Acad Sci U S A, 104, 1213-1218.
PDB code: 2nuu
17203075 O.Yildiz, C.Kalthoff, S.Raunser, and W.Kühlbrandt (2007).
Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.
  EMBO J, 26, 589-599.
PDB codes: 2j9c 2j9d 2j9e
17480017 R.Marino, D.Melillo, M.Di Filippo, A.Yamada, M.R.Pinto, R.De Santis, E.R.Brown, and G.Matassi (2007).
Ammonium channel expression is essential for brain development and function in the larva of Ciona intestinalis.
  J Comp Neurol, 503, 135-147.  
17998534 R.N.Fong, K.S.Kim, C.Yoshihara, W.B.Inwood, and S.Kustu (2007).
The W148L substitution in the Escherichia coli ammonium channel AmtB increases flux and indicates that the substrate is an ion.
  Proc Natl Acad Sci U S A, 104, 18706-18711.  
17189259 S.M.Saparov, K.Liu, P.Agre, and P.Pohl (2007).
Fast and selective ammonia transport by aquaporin-8.
  J Biol Chem, 282, 5296-5301.  
18040042 X.Li, S.Jayachandran, H.H.Nguyen, and M.K.Chan (2007).
Structure of the Nitrosomonas europaea Rh protein.
  Proc Natl Acad Sci U S A, 104, 19279-19284.
PDB codes: 3b9y 3b9z
16342219 A.Müller, Y.Zhou, H.Bögge, M.Schmidtmann, T.Mitra, E.T.Haupt, and A.Berkle (2006).
"Gating" the pores of a metal oxide based capsule: after initial cation uptake subsequent cations are found hydrated and supramolecularly fixed above the pores.
  Angew Chem Int Ed Engl, 45, 460-465.  
16477434 A.M.Marini, M.Boeckstaens, F.Benjelloun, B.Chérif-Zahar, and B.André (2006).
Structural involvement in substrate recognition of an essential aspartate residue conserved in Mep/Amt and Rh-type ammonium transporters.
  Curr Genet, 49, 364-374.  
16468990 A.Van Nuland, P.Vandormael, M.Donaton, M.Alenquer, A.Lourenço, E.Quintino, M.Versele, and J.M.Thevelein (2006).
Ammonium permease-based sensing mechanism for rapid ammonium activation of the protein kinase A pathway in yeast.
  Mol Microbiol, 59, 1485-1505.  
16467464 B.J.Monahan, M.C.Askin, M.J.Hynes, and M.A.Davis (2006).
Differential expression of Aspergillus nidulans ammonium permease genes is regulated by GATA transcription factor AreA.
  Eukaryot Cell, 5, 226-237.  
17026539 D.Loqué, L.Yuan, S.Kojima, A.Gojon, J.Wirth, S.Gazzarrini, K.Ishiyama, H.Takahashi, and N.von Wirén (2006).
Additive contribution of AMT1;1 and AMT1;3 to high-affinity ammonium uptake across the plasma membrane of nitrogen-deficient Arabidopsis roots.
  Plant J, 48, 522-534.  
16273393 F.K.Winkler (2006).
Amt/MEP/Rh proteins conduct ammonia.
  Pflugers Arch, 451, 701-707.  
16999738 H.Mitsuzawa (2006).
Ammonium transporter genes in the fission yeast Schizosaccharomyces pombe: role in ammonium uptake and a morphological transition.
  Genes Cells, 11, 1183-1195.  
16630265 J.Thornton, D.Blakey, E.Scanlon, and M.Merrick (2006).
The ammonia channel protein AmtB from Escherichia coli is a polytopic membrane protein with a cleavable signal peptide.
  FEMS Microbiol Lett, 258, 114-120.  
  16446503 M.Mayer, G.Schaaf, I.Mouro, C.Lopez, Y.Colin, P.Neumann, J.P.Cartron, and U.Ludewig (2006).
Different transport mechanisms in plant and human AMT/Rh-type ammonium transporters.
  J Gen Physiol, 127, 133-144.  
16917981 M.Mayer, and U.Ludewig (2006).
Role of AMT1;1 in NH4+ acquisition in Arabidopsis thaliana.
  Plant Biol (Stuttg), 8, 522-528.  
16595629 Q.Ji, S.Hashmi, Z.Liu, J.Zhang, Y.Chen, and C.H.Huang (2006).
CeRh1 (rhr-1) is a dominant Rhesus gene essential for embryonic development and hypodermal function in Caenorhabditis elegans.
  Proc Natl Acad Sci U S A, 103, 5881-5886.  
16814540 R.Dutzler (2006).
The ClC family of chloride channels and transporters.
  Curr Opin Struct Biol, 16, 439-446.  
17012311 T.P.Nygaard, C.Rovira, G.H.Peters, and M...Jensen (2006).
Ammonium recruitment and ammonia transport by E. coli ammonia channel AmtB.
  Biophys J, 91, 4401-4412.  
17015648 Y.Wei, G.Deikus, B.Powers, V.Shelden, T.A.Krulwich, and D.H.Bechhofer (2006).
Adaptive gene expression in Bacillus subtilis strains deleted for tetL.
  J Bacteriol, 188, 7090-7100.  
16762025 Y.Zhang, E.L.Pohlmann, M.C.Conrad, and G.P.Roberts (2006).
The poor growth of Rhodospirillum rubrum mutants lacking PII proteins is due to an excess of glutamine synthetase activity.
  Mol Microbiol, 61, 497-510.  
16227429 C.H.Huang, and J.Peng (2005).
Evolutionary conservation and diversification of Rh family genes and proteins.
  Proc Natl Acad Sci U S A, 102, 15512-15517.  
16319876 D.M.Engelman (2005).
Membranes are more mosaic than fluid.
  Nature, 438, 578-580.  
16281947 M.J.Conroy, P.A.Bullough, M.Merrick, and N.D.Avent (2005).
Modelling the human rhesus proteins: implications for structure and function.
  Br J Haematol, 131, 543-551.  
16214888 S.L.Andrade, A.Dickmanns, R.Ficner, and O.Einsle (2005).
Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus.
  Proc Natl Acad Sci U S A, 102, 14994-14999.
PDB codes: 2b2f 2b2h 2b2i 2b2j
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.