4F6T

The crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nature's Polyoxometalate Chemistry: X-ray Structure of the Mo Storage Protein Loaded with Discrete Polynuclear Mo-O Clusters.

Kowalewski, B.Poppe, J.Demmer, U.Warkentin, E.Dierks, T.Ermler, U.Schneider, K.

(2012) J.Am.Chem.Soc. 134: 9768-9774

  • DOI: 10.1021/ja303084n

  • PubMed Abstract: 
  • Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reve ...

    Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo(8), three Mo(5-7), and one Mo(3) clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)(3) protein complex. The structurally identical Mo(8) clusters (three layers of two, four, and two MoO(n) octahedra) are distinguishable from the [Mo(8)O(26)](4-) cluster formed in acidic solutions by two displaced MoO(n) octahedra implicating three kinetically labile terminal ligands. Stabilization in the covalent Mo(8) cluster is achieved by Mo bonding to Hisα156-N(ε2) and Gluα129-O(ε1). The absence of covalent protein interactions in the noncovalent Mo(8) cluster is compensated by a more extended hydrogen-bond network involving three pronounced histidines. One displaced MoO(n) octahedron might serve as nucleation site for an inhomogeneous Mo(5-7) cluster largely surrounded by bulk solvent. In the Mo(3) cluster located on the 3-fold axis, the three accurately positioned His140-N(ε2) atoms of the α subunits coordinate to the Mo atoms. The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host-guest system. Template, nucleation/protection, and catalyst functions of the polypeptide as well as perspectives for designing new clusters are discussed.


    Organizational Affiliation

    Biochemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molybdenum storage protein subunit beta
B
268Azotobacter 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
244Azotobacter 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

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Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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

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Download CCD File 
A
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
6M0
Query on 6M0

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Download CCD File 
B
MO(6)-O(26) Cluster
H16 Mo6 O26
DEGKPRAGDPFTOO-UHFFFAOYSA-A
 Ligand Interaction
8M0
Query on 8M0

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Download CCD File 
A, B
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Octamolybdate [Mo(VI)8O28]8-
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.139 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 115.740α = 90.00
b = 115.740β = 90.00
c = 233.620γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
EDNAdata collection
REFMACphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Non-polymer description