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 

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

  • 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 con ...

    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: 
    • 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.,Sect.D 64: 1172
    • 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 65: 910


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity transport system protein p37
A, B
344Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)Mutation(s): 0 
Gene Names: p37
Find proteins for Q49410 (Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195))
Go to UniProtKB:  Q49410
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
VIB
Query on VIB

Download SDF File 
Download CCD File 
A, B
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
THIAMIN, VITAMIN B1
C12 H17 N4 O S
JZRWCGZRTZMZEH-UHFFFAOYSA-N
 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.279α = 90.00
b = 90.366β = 90.00
c = 175.363γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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