4FDV

CobH from Rhodobacter capsulatus (SB1003) in complex with HBA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 933-940

  • 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 methylmutaseA209Rhodobacter 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
0UK
Query on 0UK

Download CCD File 
A
3-[(1R,2R,3R,5R,6S,7R,9Z,12S,13S,14Z,17S,18S,19R)-2,13,18-tris(2-hydroxy-2-oxoethyl)-3,12,17-tris(3-hydroxy-3-oxopropyl)-3,5,8,8,13,15,18,19-octamethyl-1,2,5,6,7,12,17,22-octahydrocorrin-7-yl]propanoic acid
C45 H62 N4 O14
YHLYHOGUCOLFRO-ZWMNGWNLSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.251α = 90
b = 66.028β = 98.98
c = 48.48γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references