PDBsum entry 2v84

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protein ligands metals links
Transport protein PDB id
Protein chain
319 a.a. *
MES ×2
_CL ×5
Waters ×128
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Crystal structure of the tp0655 (tppotd) lipoprotein of treponema pallidum
Structure: Spermidine/putrescine abc transporter, periplasmi binding protein. Chain: a. Fragment: residues 25-348. Synonym: tp0655 lipoprotein, potd. Engineered: yes. Other_details: construct used lacks the first amino acid re (i.E. Cysteine) which is post-translationally acylated.
Source: Treponema pallidum. Organism_taxid: 243276. Strain: nichols. Expressed in: escherichia coli. Expression_system_taxid: 511693. Other_details: nichols strain isolated from cerebrospinal f a neurosyphilis patient
1.78Å     R-factor:   0.236     R-free:   0.260
Authors: M.Machius,C.A.Brautigam,D.R.Tomchick,P.Ward,Z.Otwinowski,J.S R.K.Deka,M.V.Norgard
Key ref:
M.Machius et al. (2007). Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor. J Mol Biol, 373, 681-694. PubMed id: 17868688 DOI: 10.1016/j.jmb.2007.08.018
02-Aug-07     Release date:   25-Sep-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O83661  (O83661_TREPA) -  Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
348 a.a.
319 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     polyamine transport   1 term 
  Biochemical function     polyamine binding     1 term  


DOI no: 10.1016/j.jmb.2007.08.018 J Mol Biol 373:681-694 (2007)
PubMed id: 17868688  
Structural and biochemical basis for polyamine binding to the Tp0655 lipoprotein of Treponema pallidum: putative role for Tp0655 (TpPotD) as a polyamine receptor.
M.Machius, C.A.Brautigam, D.R.Tomchick, P.Ward, Z.Otwinowski, J.S.Blevins, R.K.Deka, M.V.Norgard.
Tp0655 of Treponema pallidum, the causative agent of syphilis, is predicted to be a 40 kDa membrane lipoprotein. Previous sequence analysis of Tp0655 noted its homology to polyamine-binding proteins of the bacterial PotD family, which serve as periplasmic ligand-binding proteins of ATP-binding-cassette (ABC) transport systems. Here, the 1.8 A crystal structure of Tp0655 demonstrated structural homology to Escherichia coli PotD and PotF. The latter two proteins preferentially bind spermidine and putrescine, respectively. All of these proteins contain two domains that sandwich the ligand between them. The ligand-binding site of Tp0655 can be occupied by 2-(N-morpholino)ethanesulfanoic acid, a component of the crystallization medium. To discern the polyamine binding preferences of Tp0655, the protein was subjected to isothermal titration calorimetric experiments. The titrations established that Tp0655 binds polyamines avidly, with a marked preference for putrescine (Kd=10 nM) over spermidine (Kd=430 nM), but the related compounds cadaverine and spermine did not bind. Structural comparisons and structure-based sequence analyses provide insights into how polyamine-binding proteins recognize their ligands. In particular, these comparisons allow the derivation of rules that may be used to predict the function of other members of the PotD family. The sequential, structural, and functional homology of Tp0655 to PotD and PotF prompt the conclusion that the former likely is the polyamine-binding component of an ABC-type polyamine transport system in T. pallidum. We thus rename Tp0655 as TpPotD. The ramifications of TpPotD as a polyamine-binding protein to the parasitic strategy of T. pallidum are discussed.
  Selected figure(s)  
Figure 3.
Figure 3. Structures and atom numbering convention for the polyamines studied here. The structures are aligned such that they demonstrate their respective homologies to spermidine.
Figure 5.
Figure 5. Schematic of the polyamine-binding site in Tp0655, PotD, PotF with spermidine as a reference. Listed are all residues that interact with ligand in PotD and PotF as well as structurally equivalent (based on C^α positions) residues in the other proteins. Residues in lower-case letters are structurally equivalent but their side-chains do not establish interactions with the ligand.
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 373, 681-694) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20661547 A.M.Brandt, W.Raksajit, P.Yodsang, P.Mulo, A.Incharoensakdi, T.A.Salminen, and P.Mäenpää (2010).
Characterization of the substrate-binding PotD subunit in Synechocystis sp. strain PCC 6803.
  Arch Microbiol, 192, 791-801.  
20382996 D.Borek, M.Cymborowski, M.Machius, W.Minor, and Z.Otwinowski (2010).
Diffraction data analysis in the presence of radiation damage.
  Acta Crystallogr D Biol Crystallogr, 66, 426-436.  
19432802 J.D.Radolf, and D.C.Desrosiers (2009).
Treponema pallidum, the stealth pathogen, changes, but how?
  Mol Microbiol, 72, 1081-1086.  
18405343 P.Shah, and E.Swiatlo (2008).
A multifaceted role for polyamines in bacterial pathogens.
  Mol Microbiol, 68, 4.  
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.