5C4R

CobK precorrin-6A reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.

Gu, S.Sushko, O.Deery, E.Warren, M.J.Pickersgill, R.W.

(2015) Sci Rep 5: 16943

  • DOI: 10.1038/srep16943
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenz ...

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.


    Organizational Affiliation

    Chemistry &Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent CT2 7NJ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Precorrin-6A reductase
A
251Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)Mutation(s): 0 
Gene Names: cobK
EC: 1.3.1.54
Find proteins for O68098 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Go to UniProtKB:  O68098
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.900α = 90.00
b = 75.300β = 90.00
c = 115.100γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
SHELXphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I013334/1

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence