7BBX

Neisseria gonorrhoeae transaldolase, variant K8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.119 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A lysine-cysteine redox switch with an NOS bridge regulates enzyme function.

Wensien, M.von Pappenheim, F.R.Funk, L.M.Kloskowski, P.Curth, U.Diederichsen, U.Uranga, J.Ye, J.Fang, P.Pan, K.T.Urlaub, H.Mata, R.A.Sautner, V.Tittmann, K.

(2021) Nature 593: 460-464

  • DOI: 10.1038/s41586-021-03513-3
  • Primary Citation of Related Structures:  
    6ZWF, 6ZWH, 6ZWJ, 6ZX4, 7B0L, 7BBW, 7BBX

  • PubMed Abstract: 
  • Disulfide bonds between cysteine residues are important post-translational modifications in proteins that have critical roles for protein structure and stability, as redox-active catalytic groups in enzymes or allosteric redox switches that govern protein function 1-4 ...

    Disulfide bonds between cysteine residues are important post-translational modifications in proteins that have critical roles for protein structure and stability, as redox-active catalytic groups in enzymes or allosteric redox switches that govern protein function 1-4 . In addition to forming disulfide bridges, cysteine residues are susceptible to oxidation by reactive oxygen species, and are thus central not only to the scavenging of these but also to cellular signalling and communication in biological as well as pathological contexts 5,6 . Oxidized cysteine species are highly reactive and may form covalent conjugates with, for example, tyrosines in the active sites of some redox enzymes 7,8 . However, to our knowledge, regulatory switches with covalent crosslinks other than disulfides have not previously been demonstrated. Here we report the discovery of a covalent crosslink between a cysteine and a lysine residue with a NOS bridge that serves as an allosteric redox switch in the transaldolase enzyme of Neisseria gonorrhoeae, the pathogen that causes gonorrhoea. X-ray structure analysis of the protein in the oxidized and reduced state reveals a loaded-spring mechanism that involves a structural relaxation upon redox activation, which is propagated from the allosteric redox switch at the protein surface to the active site in the protein interior. This relaxation leads to a reconfiguration of key catalytic residues and elicits an increase in enzymatic activity of several orders of magnitude. The redox switch is highly conserved in related transaldolases from other members of the Neisseriaceae; for example, it is present in the transaldolase of Neisseria meningitides (a pathogen that is the primary cause of meningitis and septicaemia in children). We surveyed the Protein Data Bank and found that the NOS bridge exists in diverse protein families across all domains of life (including Homo sapiens) and that it is often located at catalytic or regulatory hotspots. Our findings will inform strategies for the design of proteins and peptides, as well as the development of new classes of drugs and antibodies that target the lysine-cysteine redox switch 9,10 .


    Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. ktittma@gwdg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransaldolaseA352Neisseria gonorrhoeaeMutation(s): 1 
Gene Names: 
EC: 2.2.1.2
UniProt
Find proteins for Q5F6E9 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F6E9 
Go to UniProtKB:  Q5F6E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5F6E9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
C [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.119 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.42α = 90
b = 82.89β = 90
c = 90.25γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2021-05-19
    Changes: Database references
  • Version 1.3: 2021-06-02
    Changes: Database references