6GX4

The molybdenum storage protein: with ATP/Mn2+ and with POM clusters formed under in vitro conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Molybdenum Storage Protein: A soluble ATP hydrolysis-dependent molybdate pump.

Poppe, J.Brunle, S.Hail, R.Wiesemann, K.Schneider, K.Ermler, U.

(2018) FEBS J. 285: 4602-4616

  • DOI: 10.1111/febs.14684
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A continuous FeMo cofactor supply for nitrogenase maturation is ensured in Azotobacter vinelandii by developing a cage-like molybdenum storage protein (MoSto) capable to store ca. 120 molybdate molecules ( <mml:math xmlns:mml="http://www.w3.org/1998/ ...

    A continuous FeMo cofactor supply for nitrogenase maturation is ensured in Azotobacter vinelandii by developing a cage-like molybdenum storage protein (MoSto) capable to store ca. 120 molybdate molecules ( MoO 4 2 - ) as discrete polyoxometalate (POM) clusters. To gain mechanistic insight into this process, MoSto was characterized by Mo and ATP/ADP content, structural, and kinetic analysis. We defined three functionally relevant states specified by the presence of both ATP/ADP and POM clusters (MoSto funct ), of only ATP/ADP (MoSto basal ) and of neither ATP/ADP nor POM clusters (MoSto zero ), respectively. POM clusters are only produced when ATP is hydrolyzed to ADP and phosphate. V max was ca. 13 μmol phosphate ·min -1 ·mg -1 and K m for molybdate and ATP/Mg 2+ in the low micromolar range. ATP hydrolysis presumably proceeds at subunit α, inferred from a highly occupied α-ATP/Mg 2+ and a weaker occupied β-ATP/no Mg 2+ -binding site found in the MoSto funct structure. Several findings indicate that POM cluster storage is separated into a rapid ATP hydrolysis-dependent molybdate transport across the protein cage wall and a slow molybdate assembly induced by combined auto-catalytic and protein-driven processes. The cage interior, the location of the POM cluster depot, is locked in all three states and thus not rapidly accessible for molybdate from the outside. Based on V max , the entire Mo storage process should be completed in less than 10 s but requires, according to the molybdate content analysis, ca. 15 min. Long-time incubation of MoSto basal with nonphysiological high molybdate amounts implicates an equilibrium in and outside the cage and POM cluster self-formation without ATP hydrolysis. DATABASES: The crystal structures MoSto in the MoSto-F6, MoSto-F7, MoSto basal , MoSto zero , and MoSto-F1 vitro states were deposited to PDB under the accession numbers PDB 6GU5, 6GUJ, 6GWB, 6GWV, and 6GX4.


    Organizational Affiliation

    Abteilung molelukare Biowissensschaften, Molekulare Zellbiologie der Pflanzen, Goethe Universität, Frankfurt am Main, Germany.,Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.,Biochemie I, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit beta
B
269Azotobacter vinelandii (strain DJ / ATCC BAA-1303)Mutation(s): 0 
Gene Names: mosB
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Go to UniProtKB:  P84253
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit alpha
A
275Azotobacter vinelandii (strain DJ / ATCC BAA-1303)Mutation(s): 0 
Gene Names: mosA
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Go to UniProtKB:  P84308
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
FV2
Query on FV2

Download SDF File 
Download CCD File 
A
Mo8 cluster
Mo8 O30
OYDJOMQLWBZCKT-UHFFFAOYSA-A
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MOO
Query on MOO

Download SDF File 
Download CCD File 
A
MOLYBDATE ION
MOLYBDATE
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
 Ligand Interaction
FUQ
Query on FUQ

Download SDF File 
Download CCD File 
B
Mo5 Cluster
H20 Mo5 O25
KKTGFJKWMBVMER-UHFFFAOYSA-A
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.270α = 90.00
b = 114.270β = 90.00
c = 234.140γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-03-06
    Type: Data collection