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 
  • R-Value Observed: 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:  
    4AU1, 3NJR, 4FDV

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRECORRIN-8X METHYLMUTASEA229Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: cobHRCAP_rcc02046
EC: 5.4.1.2
Find proteins for D5AV08 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AV08 
Go to UniProtKB:  D5AV08
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P8X
Query on P8X

Download CCD File 
A
DESMETHYL-HBA
C44 H58 N4 O14
LIJKCTVSMYEQAC-IBWMGOEXSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.55α = 90
b = 65.71β = 99.32
c = 48.05γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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