1VA0

Crystal Structure of the Native Form of Uroporphyrin III C-methyl transferase from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus.

Rehse, P.H.Kitao, T.Tahirov, T.H.

(2005) Acta Crystallogr.,Sect.D 61: 913-919

  • DOI: 10.1107/S0907444905008838
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this pro ...

    Uroporphyrinogen-III C-methyltransferase from Thermus thermophilus is a multifunctional protein responsible for two of the eight S-adenosyl-methionine-dependent methylations of the corrin ring during vitamin B(12) synthesis. The structure of this protein has been solved to 2.0 A resolution in both the apo and cofactor-bound form. The monomer consists of two domains, A and B, each consisting of a five-stranded beta-sheet and two or three alpha-helices, with the cofactor bound at the interface. The biological unit is the dimer found in the asymmetric unit. This dimer is related by a non-crystallographic twofold such that two B domains combine to form a long ten-stranded beta-sheet. When compared with solved related structures, this structure shows clear differences in the region involved in cofactor and substrate binding, affirming the role of several previously implicated residues and questioning others. The solved related structures are characterized by an exposed active site. The T. thermophilus structure has this site restricted by the interaction of a flexible loop structure with a highly conserved residue, suggesting a mechanistic role. This structure represents the ;closed' form of the protein.


    Organizational Affiliation

    APCG, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uroporphyrin-III C-methyltransferase
A, B
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Find proteins for Q5SKH6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKH6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.500α = 90.00
b = 63.568β = 90.00
c = 131.902γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2016-09-28
    Type: Other