4AU1

Crystal Structure of CobH (precorrin-8x methyl mutase) complexed with C5 desmethyl-HBA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

An Enzyme-Trap Approach Allows Isolation of Intermediates in Cobalamin Biosynthesis

Deery, E.Schroeder, S.Lawrence, A.D.Taylor, S.L.Seyedarabi, A.Waterman, J.Wilson, K.S.Brown, D.Geeves, M.A.Howard, M.J.Pickersgill, R.W.Warren, M.J.

(2012) Nat.Chem.Biol. 8: 933

  • DOI: 10.1038/nchembio.1086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathwa ...

    The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.


    Organizational Affiliation

    School of Biosciences, University of Kent, Canterbury, Kent, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRECORRIN-8X METHYLMUTASE
A
229Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)Mutation(s): 0 
Gene Names: cobH
EC: 5.4.1.2
Find proteins for D5AV08 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Go to UniProtKB:  D5AV08
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
P8X
Query on P8X

Download SDF File 
Download CCD File 
A
DESMETHYL-HBA
C44 H58 N4 O14
LIJKCTVSMYEQAC-IBWMGOEXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.550α = 90.00
b = 65.710β = 99.32
c = 48.050γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2012-10-10
    Type: Database references
  • Version 1.2: 2012-10-17
    Type: Data collection, Database references
  • Version 1.3: 2012-11-14
    Type: Database references