6GUJ

Molybdenum storage protein with two occupied ATP binding sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    6GU5, 6GUJ, 6GWV, 6GX4

  • 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 ( MoO 4 2 - ) as discrete polyoxometalate (POM) clusters ...

    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

    Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdenum storage protein subunit betaA [auth B]269Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosBAvin_43210
UniProt
Find proteins for P84253 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84253 
Go to UniProtKB:  P84253
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84253
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alphaB [auth A]275Azotobacter vinelandii DJMutation(s): 0 
Gene Names: mosAAvin_43200
UniProt
Find proteins for P84308 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore P84308 
Go to UniProtKB:  P84308
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84308
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8M0
Query on 8M0

Download Ideal Coordinates CCD File 
D [auth B],
K [auth A]
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth B],
I [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MOO
Query on MOO

Download Ideal Coordinates CCD File 
L [auth A]MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
 Ligand Interaction
MO
Query on MO

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth B],
H [auth B],
M [auth A],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
M [auth A],
N [auth A],
O [auth A]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.15α = 90
b = 115.15β = 90
c = 234.5γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references