2UX9

Crystal structure of the T. thermophilus dodecin R65A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Dodecin from Thermus Thermophilus, a Bifunctional Cofactor Storage Protein.

Meissner, B.Schleicher, E.Weber, S.Essen, L.-O.

(2007) J Biol Chem 282: 33142

  • DOI: 10.1074/jbc.M704951200
  • Primary Citation of Related Structures:  
    2UX9, 2V18, 2V19, 2V21

  • PubMed Abstract: 
  • Dodecins are so far the smallest known flavoproteins (68-71 amino acids) and are most likely involved in prokaryotic flavin storage. The dodecin monomers adopt a simple betaalphabetabeta-fold and assemble to hollow sphere-like dodecameric complexes. Flavin binding by the dodecin from Thermus thermophilus showed a 1:1 stoichiometry and apparent dissociation constants in the submicromolar to nanomolar range as characterized by isothermal titration calorimetry and fluorescence titrations ...

    Dodecins are so far the smallest known flavoproteins (68-71 amino acids) and are most likely involved in prokaryotic flavin storage. The dodecin monomers adopt a simple betaalphabetabeta-fold and assemble to hollow sphere-like dodecameric complexes. Flavin binding by the dodecin from Thermus thermophilus showed a 1:1 stoichiometry and apparent dissociation constants in the submicromolar to nanomolar range as characterized by isothermal titration calorimetry and fluorescence titrations. The x-ray structures of the flavin-prebound and FMN-reconstituted state of the T. thermophilus dodecin revealed binding of FMN dimers in a novel si-si- rather than the re-re- orientation of their isoalloxazine moieties as found before in an archaeal dodecin. Electron paramagnetic resonance studies demonstrated that upon reduction the excess electron is localized only on one flavin, thus making dodecin-bound flavins highly refractory to redox chemistry. Besides FMN dimers, trimers of coenzyme A are additionally bound to this eubacterial dodecin along the 3-fold symmetry face II of the dodecin complex. Therefore, dodecins can act as bifunctional cofactor storage proteins that sequester catalytic cofactors in prokaryotes very efficiently in an aggregated and unreactive state.


    Organizational Affiliation

    Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, Marburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DODECIN
A, B, C, D, E, F
A, B, C, D, E, F
69Thermus thermophilus HB8Mutation(s): 1 
Gene Names: TTHA1431
UniProt
Find proteins for Q5SIE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIE3 
Go to UniProtKB:  Q5SIE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIE3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
Q [auth C],
S [auth D],
V [auth E],
I [auth A],
L [auth B],
Q [auth C],
S [auth D],
V [auth E],
Y [auth F]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
P [auth C],
R [auth D],
T [auth E],
H [auth A],
K [auth B],
P [auth C],
R [auth D],
T [auth E],
U [auth E]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C],
X [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
N [auth C],
O [auth C],
W [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.585α = 90
b = 67.585β = 90
c = 169.188γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-03
    Changes: Database references, Other
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection