3D8N

Uroporphyrinogen III Synthase-Uroporphyringen III Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex.

Schubert, H.L.Phillips, J.D.Heroux, A.Hill, C.P.

(2008) Biochemistry 47: 8648-8655

  • DOI: 10.1021/bi800635y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uroporphyrinogen III synthase (U3S) catalyzes the asymmetrical cyclization of a linear tetrapyrrole to form the physiologically relevant uroporphyrinogen III (uro'gen III) isomer during heme biosynthesis. Here, we report four apoenzyme and one produc ...

    Uroporphyrinogen III synthase (U3S) catalyzes the asymmetrical cyclization of a linear tetrapyrrole to form the physiologically relevant uroporphyrinogen III (uro'gen III) isomer during heme biosynthesis. Here, we report four apoenzyme and one product complex crystal structures of the Thermus thermophilus (HB27) U3S protein. The overlay of eight crystallographically unique U3S molecules reveals a huge range of conformational flexibility, including a "closed" product complex. The product, uro'gen III, binds between the two domains and is held in place by a network of hydrogen bonds between the product's side chain carboxylates and the protein's main chain amides. Interactions of the product A and B ring carboxylate side chains with both structural domains of U3S appear to dictate the relative orientation of the domains in the closed enzyme conformation and likely remain intact during catalysis. The product C and D rings are less constrained in the structure, consistent with the conformational changes required for the catalytic cyclization with inversion of D ring orientation. A conserved tyrosine residue is potentially positioned to facilitate loss of a hydroxyl from the substrate to initiate the catalytic reaction.


    Organizational Affiliation

    Departments of Biochemistry and Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah 84112, , USA. heidi@biochem.utah.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uroporphyrinogen-III synthase
A
286Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
EC: 4.2.1.75
Find proteins for Q72KM1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72KM1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UP3
Query on UP3

Download SDF File 
Download CCD File 
A
3,3',3'',3'''-[3,8,13,17-tetrakis(carboxymethyl)porphyrin-2,7,12,18-tetrayl]tetrapropanoic acid
C40 H38 N4 O16
VZVFNUAIRVUCEW-XFMUOGEMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.743α = 90.00
b = 66.478β = 91.76
c = 55.459γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-05-23 
  • Released Date: 2008-08-12 
  • Deposition Author(s): Schubert, H.L.

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description