Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.43 kDa 
• Atom Count: 167 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique protein chains: 1

1SX0

Solution NMR Structure and X-Ray Absorption Analysis of the C-Terminal Zinc-Binding Domain of the SecA ATPase

• PDB DOI: 10.2210/pdb1SX0/pdb
• BMRB: 6191

• Classification: PROTEIN TRANSPORT
• Mutation(s): No 


• Deposited: 2004-03-30 Released: 2004-07-06 
• Deposition Author(s): Dempsey, B.R., Wrona, M., Moulin, J.M., Gloor, G.B., Jalilehvand, F., Lajoie, G., Shaw, G.S., Shilton, B.H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Solution NMR Structure and X-ray Absorption Analysis of the C-Terminal Zinc-Binding Domain of the SecA ATPase.

Dempsey, B.R., Wrona, M., Moulin, J.M., Gloor, G.B., Jalilehvand, F., Lajoie, G., Shaw, G.S., Shilton, B.H.

(2004) Biochemistry 43: 9361-9371

• PubMed: 15260479 
• DOI: 10.1021/bi0493057
• Primary Citation of Related Structures:  
  1SX0, 1SX1


• PubMed Abstract: 
  

The solution NMR structure of a 22-residue Zn(2+)-binding domain (ZBD) from Esherichia coli preprotein translocase subunit SecA is presented. In conjunction with X-ray absorption analysis, the NMR structure shows that three cysteines and a histidine in the sequence CXCXSGX(8)CH assume a tetrahedral arrangement around the Zn(2+) atom, with an average Zn(2+)-S bond distance of 2.30 A and a Zn(2+)-N bond distance of 2.03 A. The NMR structure shows that ND1 of His20 binds to the Zn(2+) atom. The ND1-Zn(2+) bond is somewhat strained: it makes an angle of approximately 17 degrees with the plane of the ring, and it also shows a significant "in-plane" distortion of 13 degrees. A comprehensive sequence alignment of the SecA-ZBD from many different organisms shows that, along with the four Zn(2+) ligands, there is a serine residue (Ser12) that is completely conserved. The NMR structure indicates that the side chain of this serine residue forms a strong hydrogen bond with the thiolate of the third cysteine residue (Cys19); therefore, the conserved serine appears to have a critical role in the structure. SecB, an export-specific chaperone, is the only known binding partner for the SecA-ZBD. A phylogenetic analysis using 86 microbial genomes shows that 59 of the organisms carry SecA with a ZBD, but only 31 of these organisms also possess a gene for SecB, indicating that there may be uncharacterized binding partners for the SecA-ZBD.

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Organizational Affiliation: 

Department of Biochemistry, University of Western Ontario, London ON N6A 5C1, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SecA	A	22	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 1SX0 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-30 
• Released Date: 2004-07-06 
Deposition Author(s): Dempsey, B.R., Wrona, M., Moulin, J.M., Gloor, G.B., Jalilehvand, F., Lajoie, G., Shaw, G.S., Shilton, B.H.

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations