6RKE | pdb_00006rke

Molybdenum storage protein - P212121, ADP, molybdate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.214 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.

Brunle, S.Eisinger, M.L.Poppe, J.Mills, D.J.Langer, J.D.Vonck, J.Ermler, U.

(2019) Proc Natl Acad Sci U S A 

  • DOI: https://doi.org/10.1073/pnas.1913031116
  • Primary Citation Related Structures: 
    6RIS, 6RJ4, 6RKD, 6RKE

  • PubMed Abstract: 

    The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) 3 cage-like protein complex under ATP consumption. Here, we suggest a unique mechanism for the ATP-powered molybdate pumping process based on X-ray crystallography, cryoelectron microscopy, hydrogen-deuterium exchange mass spectrometry, and mutational studies of MoSto from Azotobacter vinelandii . First, we show that molybdate, ATP, and Mg 2+ consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.


  • Organizational Affiliation
    • Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 373.43 kDa 
  • Atom Count: 26,584 
  • Modeled Residue Count: 3,238 
  • Deposited Residue Count: 3,264 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit beta269Azotobacter 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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alpha275Azotobacter 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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LHW

Query on LHW



Download:Ideal Coordinates CCD File
EA [auth C],
NB [auth K]
MO(10)-O(35) Cluster
H16 Mo10 O35
QLJDKXQFXYWLGK-UHFFFAOYSA-A
8M0

Query on 8M0



Download:Ideal Coordinates CCD File
AA [auth C]
DA [auth C]
DB [auth I]
GB [auth L]
HA [auth F]
AA [auth C],
DA [auth C],
DB [auth I],
GB [auth L],
HA [auth F],
MA [auth E],
MB [auth K],
O [auth B],
PA [auth H],
U [auth A],
UA [auth G],
XA [auth J]
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
LJB

Query on LJB



Download:Ideal Coordinates CCD File
JB [auth L],
R [auth B]
MO(8)-O(26) Cluster
H15 Mo8 O26
BTBGOQYWAXYGKM-UHFFFAOYSA-A
ATP

Query on ATP



Download:Ideal Coordinates CCD File
BA [auth C]
BB [auth I]
KA [auth E]
KB [auth K]
S [auth A]
BA [auth C],
BB [auth I],
KA [auth E],
KB [auth K],
S [auth A],
SA [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
M10

Query on M10



Download:Ideal Coordinates CCD File
V [auth A],
VA [auth G]
(mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI)
Mo3 O13
HGNGIYFURFJYFJ-UHFFFAOYSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
EB [auth L]
FA [auth F]
M [auth B]
NA [auth H]
W [auth D]
EB [auth L],
FA [auth F],
M [auth B],
NA [auth H],
W [auth D],
WA [auth J]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MOO
(Subject of Investigation/LOI)

Query on MOO



Download:Ideal Coordinates CCD File
HB [auth L]
IA [auth F]
P [auth B]
QA [auth H]
Y [auth D]
HB [auth L],
IA [auth F],
P [auth B],
QA [auth H],
Y [auth D],
ZA [auth J]
MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
AB [auth J]
IB [auth L]
JA [auth F]
Q [auth B]
RA [auth H]
AB [auth J],
IB [auth L],
JA [auth F],
Q [auth B],
RA [auth H],
Z [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth C]
CB [auth I]
FB [auth L]
GA [auth F]
LA [auth E]
CA [auth C],
CB [auth I],
FB [auth L],
GA [auth F],
LA [auth E],
LB [auth K],
N [auth B],
OA [auth H],
T [auth A],
TA [auth G],
X [auth D],
YA [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.214 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.06α = 90
b = 148.86β = 90
c = 183.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description