3MYU

Mycoplasma genitalium MG289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein.

Sippel, K.H.Venkatakrishnan, B.Boehlein, S.K.Sankaran, B.Quirit, J.G.Govindasamy, L.Agbandje-McKenna, M.Goodison, S.Rosser, C.J.McKenna, R.

(2011) Proteins 79: 528-536

  • DOI: 10.1002/prot.22900
  • Primary Citation of Related Structures:  
    3MYU

  • PubMed Abstract: 
  • Mycoplasma genitalium is one of the smallest organisms capable of self-replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes ...

    Mycoplasma genitalium is one of the smallest organisms capable of self-replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes. The crystal structure of MG289 has been solved at 1.95 Å resolution. The structurally identified thiamine binding region reveals possible mechanisms for ligand promiscuity. MG289 was determined to be an extracytoplasmic thiamine binding lipoprotein. Computational analysis, size exclusion chromatography, and small angle X-ray scattering indicates that MG289 homodimerizes in a concentration-dependant manner. Comparisons to the thiamine pyrophosphate binding homolog Cypl reveal insights into the metabolic differences between mycoplasmal species including identifying possible kinases for cofactor phosphorylation and describing the mechanism of thiamine transport into the cell. These results provide a baseline to build our understanding of the minimal metabolic requirements of a living organism.


    Related Citations: 
    • Cloning, expression, purification, crystallization and preliminary X-ray analysis of Mycoplasma genitalium protein MG289.
      Sippel, K.H., Boehlein, S.K., Sakai, Y., Quirit, J.G., Agbandje-McKenna, M., Rosser, C.J., McKenna, R.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 910
    • Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis.
      Sippel, K.H., Robbins, A.H., Reutzel, R., Boehlein, S.K., Namiki, K., Goodison, S., Agbandje-McKenna, M., Rosser, C.J., McKenna, R.
      (2009) J Bacteriol 191: 2585
    • Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37.
      Sippel, K.H., Robbins, A.H., Reutzel, R., Domsic, J., Boehlein, S.K., Govindasamy, L., Agbandje-McKenna, M., Rosser, C.J., McKenna, R.
      (2008) Acta Crystallogr D Biol Crystallogr 64: 1172

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, College of Medicine, Gainesville, Florida 32610, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity transport system protein p37A, B344Mycoplasma genitaliumMutation(s): 0 
Gene Names: MG289p37
Find proteins for Q49410 (Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195))
Explore Q49410 
Go to UniProtKB:  Q49410
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIB
Query on VIB

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.279α = 90
b = 90.366β = 90
c = 175.363γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary