1K0F

Crystal structure of Zn(II)-free T. pallidum TroA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of Zn(II)-free Treponema pallidum TroA, a periplasmic metal-binding protein, reveals a closed conformation.

Lee, Y.H.Dorwart, M.R.Hazlett, K.R.Deka, R.K.Norgard, M.V.Radolf, J.D.Hasemann, C.A.

(2002) J.Bacteriol. 184: 2300-2304

  • DOI: 10.1128/jb.184.8.2300-2304.2002

  • PubMed Abstract: 
  • We previously demonstrated that Treponema pallidum TroA is a periplasmic metal-binding protein (MBP) with a distinctive alpha-helical backbone. To better understand the mechanisms of metal binding and release by TroA, we determined the crystal struct ...

    We previously demonstrated that Treponema pallidum TroA is a periplasmic metal-binding protein (MBP) with a distinctive alpha-helical backbone. To better understand the mechanisms of metal binding and release by TroA, we determined the crystal structure of the apoprotein at a resolution of 2.5 A and compared it to that of the Zn(II)-bound form (Protein Data Bank accession code 1toa). apo-TroA shows a conformation even more closed than that of its Zn(II)-bound counterpart due to a 4 degrees tilt of the C-terminal domain (residues 190 through 308) about an axis parallel to the poorly flexible backbone helix. This domain tilting pushes two loops (residues 248 through 253 and 277 through 286) towards the metal-binding site by more than 1 A, resulting in an unfavorable interaction of I251 with D66. To avoid this contact, D66 shifts towards H68, one of the four Zn(II)-coordinating residues. The approach of this negative charge coincides with the flipping of the imidazole side chain of H68, resulting in the formation of a new hydrogen bond. The conformational change of H68, along with a slight rearrangement of D279, a C-terminal domain Zn(II)-coordinating residue, distorts the metal-binding site geometry, presumably causing the release of the bound metal ion. Ligand binding and release by TroA, and presumably by other members of the MBP cluster, differs from the "Venus flytrap" mechanism utilized by bacterial nonmetal solute-binding receptors.


    Related Citations: 
    • Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone
      Lee, Y.H.,Deka, R.K.,Norgard, M.V.,Radolf, J.D.,Hasemann, C.A.
      (1999) Nat.Struct.Mol.Biol. 6: 628


    Organizational Affiliation

    Department of Biochemistry, The University of Missouri-Columbia, Columbia, Missouri 65211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic zinc-binding protein troA
A
277Treponema pallidum (strain Nichols)Mutation(s): 0 
Gene Names: troA (troMP1)
Find proteins for P96116 (Treponema pallidum (strain Nichols))
Go to UniProtKB:  P96116
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.360α = 90.00
b = 38.350β = 104.11
c = 104.470γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance