6RKD

Molybdenum storage protein under turnover conditions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit alpha
A, C, E, G, I
A, C, E, G, I, K
276Azotobacter 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdenum storage protein subunit beta
B, D, F, H, J
B, D, F, H, J, L
270Azotobacter 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
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8M0
Query on 8M0

Download Ideal Coordinates CCD File 
DB [auth F]
EA [auth C]
HB [auth G]
HC [auth J]
NC [auth K]
DB [auth F],
EA [auth C],
HB [auth G],
HC [auth J],
NC [auth K],
O [auth A],
PA [auth D],
SB [auth H],
UA [auth E],
WC [auth L],
YB [auth I],
Z [auth B]
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
J8E
Query on J8E

Download Ideal Coordinates CCD File 
BA [auth B]
FA [auth C]
IB [auth G]
JA [auth D]
JC [auth J]
BA [auth B],
FA [auth C],
IB [auth G],
JA [auth D],
JC [auth J],
OC [auth K],
P [auth A],
RC [auth L],
UB [auth H],
VA [auth E],
YA [auth F],
ZB [auth I]
oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum
H2 Mo4 O10
DPQAEXIBFYBKAN-UHFFFAOYSA-G
ATP
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth C]
CB [auth F]
FB [auth G]
GC [auth J]
LC [auth K]
CA [auth C],
CB [auth F],
FB [auth G],
GC [auth J],
LC [auth K],
M [auth A],
OA [auth D],
RB [auth H],
SA [auth E],
VC [auth L],
WB [auth I],
Y [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MOO
Query on MOO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth F]
AC [auth I]
BB [auth F]
BC [auth I]
AA [auth B],
AB [auth F],
AC [auth I],
BB [auth F],
BC [auth I],
CC [auth I],
DC [auth J],
EB [auth F],
EC [auth J],
FC [auth J],
GA [auth C],
HA [auth C],
IC [auth J],
JB [auth G],
KA [auth D],
KB [auth G],
LA [auth D],
LB [auth G],
MA [auth D],
NA [auth D],
NB [auth H],
OB [auth H],
PB [auth H],
PC [auth K],
Q [auth A],
QA [auth D],
QB [auth H],
QC [auth K],
R [auth A],
SC [auth L],
T [auth A],
TB [auth H],
TC [auth L],
U [auth B],
UC [auth L],
V [auth B],
W [auth B],
WA [auth E],
X [auth B],
XA [auth E],
XC [auth L],
ZA [auth F]
MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
OMO
Query on OMO

Download Ideal Coordinates CCD File 
IA [auth C]
KC [auth K]
MB [auth G]
RA [auth E]
S [auth A]
IA [auth C],
KC [auth K],
MB [auth G],
RA [auth E],
S [auth A],
VB [auth I]
MO(VI)(=O)(OH)2 CLUSTER
H2 Mo O3
GKDPEXRCAVYDOG-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth C]
GB [auth G]
MC [auth K]
N [auth A]
TA [auth E]
DA [auth C],
GB [auth G],
MC [auth K],
N [auth A],
TA [auth E],
XB [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release