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PDBsum entry 2vkj

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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
2vkj
Jmol
Contents
Protein chains
106 a.a.
Ligands
SO4 ×3
Waters ×215
PDB id:
2vkj
Name: Membrane protein
Title: Structure of the soluble domain of the membrane protein tm1634 from thermotoga maritima
Structure: Tm1634. Chain: a, b. Fragment: soluble domain, residues 27-128. Engineered: yes. Other_details: additional residues gshm at n-terminus
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.65Å     R-factor:   0.205     R-free:   0.229
Authors: C.J.Mccleverty,L.Columbus,A.Kreusch,S.A.Lesley,Joint Center Structural Genomics (Jcsg)
Key ref:
C.J.McCleverty et al. (2008). Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634. Protein Sci, 17, 869-877. PubMed id: 18369189 DOI: 10.1110/ps.083432208
Date:
19-Dec-07     Release date:   08-Apr-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam  
Q9X1W9  (Q9X1W9_THEMA) -  Uncharacterized protein
Seq:
Struc:
128 a.a.
106 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1110/ps.083432208 Protein Sci 17:869-877 (2008)
PubMed id: 18369189  
 
 
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634.
C.J.McCleverty, L.Columbus, A.Kreusch, S.A.Lesley.
 
  ABSTRACT  
 
As a part of the Joint Center for Structural Genomics (JCSG) biological targets, the structures of soluble domains of membrane proteins from Thermotoga maritima were pursued. Here, we report the crystal structure of the soluble domain of TM1634, a putative membrane protein of 128 residues (15.1 kDa) and unknown function. The soluble domain of TM1634 is an alpha-helical dimer that contains a single tetratrico peptide repeat (TPR) motif in each monomer where each motif is similar to that found in Tom20. The overall fold, however, is unique and a DALI search does not identify similar folds beyond the 38-residue TPR motif. Two different putative ligand binding sites, in which PEG200 and Co(2+) were located, were identified using crystallography and NMR, respectively.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. PEG200 binding site in the 26TM1634 crystal structure. D49, Y45, K74, S77, L78, F97, and K100 form the PEG200 binding site in the crystal. The 2FoFc electron density for the PEG200 is contoured at 1 and the PEG200 molecule rendered as sticks. The protein backbone is rendered as a cartoon. The side chains are rendered as sticks with transparent spheres, labeled, and colored by atom (C, gray; N, blue; and O, red). Distances (Å) between atoms are indicated by dashed lines and labeled.
Figure 6.
Figure 6. 26TM1634 binds Co^2+ in solution. (A) A native gel of 26TM1634 incubated with different ions. (B) Two-dimensional ^15N,^1H-HSQC spectra of ^15N-labeled 26TM1634. The red spectrum is without Co^2+ and the black spectrum is with 600 µM CoCl[2] added. The panels on the right correspond to the boxes drawn on the entire spectrum and the peaks are labeled with the residue assignment, and an additional spectrum recorded with 300 µM CoCl[2] is shown in orange. (C) The 26TM1634 crystal structure with the region in which chemical shifts were observed in the presence of Co^2+. E87 and D84 are rendered as sticks. (D) A 90° rotation of the protein in panel C.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2008, 17, 869-877) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18931379 F.Kiefer, K.Arnold, M.Künzli, L.Bordoli, and T.Schwede (2009).
The SWISS-MODEL Repository and associated resources.
  Nucleic Acids Res, 37, D387-D392.  
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