1S9U

Atomic structure of a putative anaerobic dehydrogenase component


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway.

Qiu, Y.Zhang, R.Binkowski, T.A.Tereshko, V.Joachimiak, A.Kossiakoff, A.

(2008) Proteins 71: 525-533

  • DOI: 10.1002/prot.21828
  • Primary Citation of Related Structures:  
    1S9U

  • PubMed Abstract: 
  • The DmsD protein is necessary for the biogenesis of dimethyl sulphoxide (DMSO) reductase in many prokaryotes. It performs a critical chaperone function initiated through its binding to the twin-arginine signal peptide of DmsA, the catalytic subunit of DMSO reductase ...

    The DmsD protein is necessary for the biogenesis of dimethyl sulphoxide (DMSO) reductase in many prokaryotes. It performs a critical chaperone function initiated through its binding to the twin-arginine signal peptide of DmsA, the catalytic subunit of DMSO reductase. Upon binding to DmsD, DmsA is translocated to the periplasm via the so-called twin-arginine translocation (Tat) pathway. Here we report the 1.38 A crystal structure of the protein DmsD from Salmonella typhimurium and compare it with a close functional homolog, TorD. DmsD has an all-alpha fold structure with a notable helical extension located at its N-terminus with two solvent exposed hydrophobic residues. A major difference between DmsD and TorD is that TorD structure is a domain-swapped dimer, while DmsD exists as a monomer. Nevertheless, these two proteins have a number of common features suggesting they function by using similar mechanisms. A possible signal peptide-binding site is proposed based on structural similarities. Computational analysis was used to identify a potential GTP binding pocket on similar surfaces of DmsD and TorD structures.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative component of anaerobic dehydrogenasesA207Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: dmsDSTM1495
Find proteins for Q8ZPK0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZPK0 
Go to UniProtKB:  Q8ZPK0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.401α = 90
b = 79.355β = 115.14
c = 43.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance