Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.70 kDa 
• Atom Count: 1953 
• Modelled Residue Count: 201 
• Deposited Residue Count: 207 
• Unique protein chains: 1

1S9U

Atomic structure of a putative anaerobic dehydrogenase component

• DOI: 10.2210/pdb1S9U/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-02-05 Released: 2004-06-08 
• Deposition Author(s): Qiu, Y., Zhang, R., Tereshko, V., Kim, Y., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

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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 

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

• PubMed: 18175314 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative component of anaerobic dehydrogenases	A	207	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: dmsD, STM1495
Find proteins for Q8ZPK0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPK0  Go to UniProtKB:  Q8ZPK0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 85.401	α = 90
b = 79.355	β = 115.14
c = 43.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-05 
• Released Date: 2004-06-08 
Deposition Author(s): Qiu, Y., Zhang, R., Tereshko, V., Kim, Y., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• 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