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: 20.88 kDa 
• Atom Count: 1463 
• Modelled Residue Count: 196 
• Deposited Residue Count: 196 
• Unique protein chains: 1

2KFW

Solution structure of full-length SlyD from E.coli

• PDB DOI: 10.2210/pdb2KFW/pdb
• BMRB: 16240

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-28 Released: 2009-09-15 
• Deposition Author(s): Martino, L., He, Y., Hands-Taylor, K.L., Valentine, E.R., Kelly, G., Giancola, C., Conte, M.R.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity.

Martino, L., He, Y., Hands-Taylor, K.L., Valentine, E.R., Kelly, G., Giancola, C., Conte, M.R.

(2009) FEBS J 276: 4529-4544

• PubMed: 19645725 
• DOI: 10.1111/j.1742-4658.2009.07159.x
• Primary Citation of Related Structures:  
  2KFW


• PubMed Abstract: 
  

The sensitive to lysis D (SlyD) protein from Escherichia coli is related to the FK506-binding protein family, and it harbours both peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone-like activity, preventing aggregation and promoting the correct folding of other proteins. Whereas a functional role of SlyD as a protein-folding catalyst in vivo remains unclear, SlyD has been shown to be an essential component for [Ni-Fe]-hydrogenase metallocentre assembly in bacteria. Interestingly, the isomerase activity of SlyD is uniquely modulated by nickel ions, which possibly regulate its functions in response to external stimuli. In this work, we investigated the solution structure of SlyD and its interaction with nickel ions, enabling us to gain insights into the molecular mechanism of this regulation. We have revealed that the PPIase module of SlyD contains an additional C-terminal alpha-helix packed against the catalytic site of the domain; unexpectedly, our results show that the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket. We suggest that such conformational rearrangements upon metal binding underlie the ability of nickel ions to regulate the isomerase activity of SlyD.

---

Organizational Affiliation: 

Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FKBP-type peptidyl-prolyl cis-trans isomerase slyD	A	196	Escherichia coli	Mutation(s): 0  Gene Names: slyD, b3349, JW3311 EC: 5.2.1.8
UniProt
Find proteins for P0A9K9 (Escherichia coli (strain K12)) Explore P0A9K9  Go to UniProtKB:  P0A9K9

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KFW Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-28 
• Released Date: 2009-09-15 
Deposition Author(s): Martino, L., He, Y., Hands-Taylor, K.L., Valentine, E.R., Kelly, G., Giancola, C., Conte, M.R.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations, Other