5K94 | pdb_00005k94

Deletion-Insertion Chimera of MBP with the Preprotein Cross-Linking Domain of the SecA ATPase

• PDB DOI: https://doi.org/10.2210/pdb5K94/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-31 Released: 2017-06-07 
• Deposition Author(s): Shilton, B.H., Hackett, J., Ghonaim, N.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Characterization of a polypeptide-binding site in the DEAD Motor of the SecA ATPase.

Khalili Yazdi, A., Namjoshi, S., Hackett, J., Ghonaim, N., Shilton, B.H.

(2017) FEBS Lett 591: 3378-3390

• PubMed: 28862749 
• DOI: https://doi.org/10.1002/1873-3468.12832
• Primary Citation of Related Structures:  
  5K94


• PubMed Abstract: 
  

  We coupled peptides from a CNBr digest of signal-sequenceless maltose-binding protein (MBP) to a surface plasmon resonance chip. SecA-N95, SecA-N68, and SecA-DM (which consists of only the DEAD Motor domains NBD1 and NBD2) bound to the immobilized peptides; ADP weakened the binding. SecA-DM, which lacks the 'preprotein cross-linking domain' (PPXD), displayed the most extensive binding, while an MBP-PPXD chimera showed no binding, demonstrating that the PPXD does not contribute to the binding. We characterized the sequence specificity using oriented peptide libraries; these results enabled synthesis of a 20-residue peptide that was used to recapitulate the results obtained with MBP-derived peptides. This study shows that there is a promiscuous and nucleotide-modulated peptide-binding site in the DEAD Motor domains of SecA.

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Organizational Affiliation: 

Department of Biochemistry, University of Western Ontario, London, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.42 kDa 
• Atom Count: 8,428 
• Modelled Residue Count: 1,012 
• Deposited Residue Count: 1,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein	A, B	508	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, secA, Z0108, ECs0102 EC: 7.4.2.8
UniProt
Find proteins for P10408 (Escherichia coli (strain K12)) Explore P10408  Go to UniProtKB:  P10408
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
UniProt Groups	P10408P0AEX9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	C [auth A], D [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.88	α = 90
b = 165.26	β = 90
c = 43.82	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Shilton, B.H., Hackett, J., Ghonaim, N.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	217494

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2018-09-19
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description