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PDBsum entry 1tlz

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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
1tlz
Jmol
Contents
Protein chains
251 a.a. *
Ligands
URI ×2
Waters ×16
* Residue conservation analysis
PDB id:
1tlz
Name: Membrane protein
Title: Tsx structure complexed with uridine
Structure: Nucleoside-specific channel-forming protein tsx. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: tsx, nupa, b0411, z0512, ecs0464, sf0348, s0356. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.10Å     R-factor:   0.276     R-free:   0.299
Authors: J.Ye,B.Van Den Berg
Key ref:
J.Ye and B.van den Berg (2004). Crystal structure of the bacterial nucleoside transporter Tsx. EMBO J, 23, 3187-3195. PubMed id: 15272310 DOI: 10.1038/sj.emboj.7600330
Date:
10-Jun-04     Release date:   24-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A927  (TSX_ECOLI) -  Nucleoside-specific channel-forming protein tsx
Seq:
Struc:
294 a.a.
251 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     transport   6 terms 
  Biochemical function     nucleoside transmembrane transporter activity     3 terms  

 

 
DOI no: 10.1038/sj.emboj.7600330 EMBO J 23:3187-3195 (2004)
PubMed id: 15272310  
 
 
Crystal structure of the bacterial nucleoside transporter Tsx.
J.Ye, B.van den Berg.
 
  ABSTRACT  
 
Tsx is a nucleoside-specific outer membrane (OM) transporter of Gram-negative bacteria. We present crystal structures of Escherichia coli Tsx in the absence and presence of nucleosides. These structures provide a mechanism for nucleoside transport across the bacterial OM. Tsx forms a monomeric, 12-stranded beta-barrel with a long and narrow channel spanning the outer membrane. The channel, which is shaped like a keyhole, contains several distinct nucleoside-binding sites, two of which are well defined. The base moiety of the nucleoside is located in the narrow part of the keyhole, while the sugar occupies the wider opening. Pairs of aromatic residues and flanking ionizable residues are involved in nucleoside binding. Nucleoside transport presumably occurs by diffusion from one binding site to the next.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Nucleoside-binding sites in the Tsx channel. (A) Surface representation viewed from the extracellular side colored as in Figure 1, showing the keyhole shape of the Tsx pore (left panel). The right panel shows a close-up of the channel with the nucleoside bound at Nuc1. (B) Cut-away side view in stereo with a difference (f[o]-f[c]) map contoured at 3 , showing the nucleoside-binding sites in thymidine-soaked crystals. The nucleosides that could be built in the density at Nuc1 and Nuc2 are shown in green. The aromatic residues that line the channel and that are involved in nucleoside binding are indicated in cyan. The front (F) and the back (B) of the barrel are indicated.
Figure 4.
Figure 4 Detailed stereoviews of the nucleoside-binding sites at Nuc1 (top panels) and Nuc2 (bottom panels), viewed in approximately the same orientations as in Figure 2A and with 2f[o]-f[c] density contoured at 1.6 in pink. Hydrogen bonds between nucleosides (green) and residues that line the channel (cyan) are indicated as dashed lines. Nitrogen atoms are shown in blue and oxygen atoms in red. Putative water molecules are shown as red spheres.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3187-3195) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20579361 A.Güven, M.Fioroni, B.Hauer, and U.Schwaneberg (2010).
Molecular understanding of sterically controlled compound release through an engineered channel protein (FhuA).
  J Nanobiotechnology, 8, 14.  
20351243 M.Tanabe, C.M.Nimigean, and T.M.Iverson (2010).
Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
  Proc Natl Acad Sci U S A, 107, 6811-6816.
PDB codes: 3a2r 3a2s 3a2t 3a2u 3vzt 3vzu 3vzw
20538726 T.C.Freeman, and W.C.Wimley (2010).
A highly accurate statistical approach for the prediction of transmembrane beta-barrels.
  Bioinformatics, 26, 1965-1974.  
20712618 T.Möhlmann, C.Bernard, S.Hach, and H.Ekkehard Neuhaus (2010).
Nucleoside transport and associated metabolism.
  Plant Biol (Stuttg), 12, 26-34.  
19371766 C.De Vocht, A.Ranquin, R.Willaert, J.A.Van Ginderachter, T.Vanhaecke, V.Rogiers, W.Versées, P.Van Gelder, and J.Steyaert (2009).
Assessment of stability, toxicity and immunogenicity of new polymeric nanoreactors for use in enzyme replacement therapy of MNGIE.
  J Control Release, 137, 246-254.  
19182779 E.M.Hearn, D.R.Patel, B.W.Lepore, M.Indic, and B.van den Berg (2009).
Transmembrane passage of hydrophobic compounds through a protein channel wall.
  Nature, 458, 367-370.
PDB codes: 2r4l 2r4n 2r4o 2r4p 2r88 3dwn 3dwo
19751218 J.K.Crane, and I.Shulgina (2009).
Feedback effects of host-derived adenosine on enteropathogenic Escherichia coli.
  FEMS Immunol Med Microbiol, 57, 214-228.  
18559855 E.M.Hearn, D.R.Patel, and B.van den Berg (2008).
Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
  Proc Natl Acad Sci U S A, 105, 8601-8606.
PDB codes: 3bry 3brz 3bs0
18611376 S.Biswas, M.M.Mohammad, L.Movileanu, and B.van den Berg (2008).
Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa.
  Structure, 16, 1027-1035.
PDB code: 2qtk
17253988 M.Traub, M.Flörchinger, J.Piecuch, H.H.Kunz, A.Weise-Steinmetz, J.W.Deitmer, H.Ekkehard Neuhaus, and T.Möhlmann (2007).
The fluorouridine insensitive 1 (fur1) mutant is defective in equilibrative nucleoside transporter 3 (ENT3), and thus represents an important pyrimidine nucleoside uptake system in Arabidopsis thaliana.
  Plant J, 49, 855-864.  
17114261 S.Tamber, E.Maier, R.Benz, and R.E.Hancock (2007).
Characterization of OpdH, a Pseudomonas aeruginosa porin involved in the uptake of tricarboxylates.
  J Bacteriol, 189, 929-939.  
16885434 D.S.Kim, Y.Chao, and M.H.Saier (2006).
Protein-translocating trimeric autotransporters of gram-negative bacteria.
  J Bacteriol, 188, 5655-5667.  
16541102 G.Sulzenbacher, S.Canaan, Y.Bordat, O.Neyrolles, G.Stadthagen, V.Roig-Zamboni, J.Rauzier, D.Maurin, F.Laval, M.Daffé, C.Cambillau, B.Gicquel, Y.Bourne, and M.Jackson (2006).
LppX is a lipoprotein required for the translocation of phthiocerol dimycocerosates to the surface of Mycobacterium tuberculosis.
  EMBO J, 25, 1436-1444.
PDB code: 2byo
16414958 H.Hong, D.R.Patel, L.K.Tamm, and B.van den Berg (2006).
The outer membrane protein OmpW forms an eight-stranded beta-barrel with a hydrophobic channel.
  J Biol Chem, 281, 7568-7577.
PDB codes: 2f1t 2f1v
16927262 O.Onaca, M.Nallani, S.Ihle, A.Schenk, and U.Schwaneberg (2006).
Functionalized nanocompartments (Synthosomes): limitations and prospective applications in industrial biotechnology.
  Biotechnol J, 1, 795-805.  
16888630 O.Yildiz, K.R.Vinothkumar, P.Goswami, and W.Kühlbrandt (2006).
Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation.
  EMBO J, 25, 3702-3713.
PDB codes: 2iwv 2iww
16418175 R.K.Deka, C.A.Brautigam, X.F.Yang, J.S.Blevins, M.Machius, D.R.Tomchick, and M.V.Norgard (2006).
The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum.
  J Biol Chem, 281, 8072-8081.
PDB codes: 2fqw 2fqx 2fqy
16489221 S.A.Bucarey, N.A.Villagra, J.A.Fuentes, and G.C.Mora (2006).
The cotranscribed Salmonella enterica sv. Typhi tsx and impX genes encode opposing nucleoside-specific import and export proteins.
  Genetics, 173, 25-34.  
16352820 S.Tamber, M.M.Ochs, and R.E.Hancock (2006).
Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa.
  J Bacteriol, 188, 45-54.  
16434398 U.Zachariae, T.Klühspies, S.De, H.Engelhardt, and K.Zeth (2006).
High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32.
  J Biol Chem, 281, 7413-7420.
PDB codes: 2fgq 2fgr
15769290 A.G.Garrow, A.Agnew, and D.R.Westhead (2005).
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.
  BMC Bioinformatics, 6, 56.  
15980452 A.G.Garrow, A.Agnew, and D.R.Westhead (2005).
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins.
  Nucleic Acids Res, 33, W188-W192.  
16302967 C.Klammt, D.Schwarz, K.Fendler, W.Haase, V.Dötsch, and F.Bernhard (2005).
Evaluation of detergents for the soluble expression of alpha-helical and beta-barrel-type integral membrane proteins by a preparative scale individual cell-free expression system.
  FEBS J, 272, 6024-6038.  
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.