7YZM

MgADPNP-bound DCCP:DCCP-R complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for coupled ATP-driven electron transfer in the double-cubane cluster protein.

Jeoung, J.H.Nicklisch, S.Dobbek, H.

(2022) Proc Natl Acad Sci U S A 119: e2203576119-e2203576119

  • DOI: https://doi.org/10.1073/pnas.2203576119
  • Primary Citation of Related Structures:  
    7YYL, 7YZM, 7YZQ

  • PubMed Abstract: 

    Electron transfers coupled to the hydrolysis of ATP allow various metalloenzymes to catalyze reductions at very negative reduction potentials. The double-cubane cluster protein (DCCP) catalyzes the reduction of small molecules, such as acetylene and hydrazine, with electrons provided by its cognate ATP-hydrolyzing reductase (DCCP-R). How ATP-driven electron transfer occurs is not known. To resolve the structural basis for ATP-driven electron transfer, we solved the structures of the DCCP:DCCP-R complex in three different states. The structures show that the DCCP-R homodimer is covalently bridged by a [4Fe4S] cluster that is aligned with the twofold axis of the DCCP homodimer, positioning the [4Fe4S] cluster to enable electron transfer to both double-cubane clusters in the DCCP dimer. DCCP and DCCP-R form stable complexes independent of oxidation state or nucleotides present, and electron transfer requires the hydrolysis of ATP. Electron transfer appears to be additionally driven by modulating the angle between the helices binding the [4Fe4S] cluster. We observed hydrogen bond networks running from the ATP binding site via the [4Fe4S] cluster in DCCP-R to the double-cubane cluster in DCCP, allowing the propagation of conformational changes. Remarkable similarities between the DCCP:DCCP-R complex and the nonhomologous nitrogenases suggest a convergent evolution of catalytic strategies to achieve ATP-driven electron transfers between iron-sulfur clusters.


  • Organizational Affiliation

    Department of Biology, Humboldt-Universität zu Berlin, 10099 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydratase family proteinA,
B,
E [auth C],
F [auth D]
422Carboxydothermus hydrogenoformans Z-2901Mutation(s): 0 
Gene Names: CHY_0487
UniProt
Find proteins for Q3AET9 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Explore Q3AET9 
Go to UniProtKB:  Q3AET9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3AET9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative CoA-substrate-specific enzyme activaseC [auth G],
D [auth H],
G [auth E],
H [auth F]
243Carboxydothermus hydrogenoformans Z-2901Mutation(s): 0 
Gene Names: CHY_0488
UniProt
Find proteins for Q3AET8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Explore Q3AET8 
Go to UniProtKB:  Q3AET8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3AET8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BJ8 (Subject of Investigation/LOI)
Query on BJ8

Download Ideal Coordinates CCD File 
I [auth A],
MA [auth C],
S [auth B],
VA [auth D]
Double cubane cluster
Fe8 S9
CSVVAMDLRWBOEA-UHFFFAOYSA-N
ANP
Query on ANP

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AA [auth G],
FB [auth E],
JA [auth H],
KB [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SF4
Query on SF4

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DB [auth E],
HA [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
TAM
Query on TAM

Download Ideal Coordinates CCD File 
CB [auth D],
V [auth B]
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
PEG
Query on PEG

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N [auth A],
O [auth A],
RA [auth C],
ZA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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BA [auth G]
GB [auth E]
IB [auth F]
J [auth A]
L [auth A]
BA [auth G],
GB [auth E],
IB [auth F],
J [auth A],
L [auth A],
LB [auth F],
M [auth A],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth C],
T [auth B],
U [auth B],
WA [auth D],
YA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BU3
Query on BU3

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
DA [auth G]
EA [auth G]
FA [auth G]
AB [auth D],
BB [auth D],
DA [auth G],
EA [auth G],
FA [auth G],
GA [auth G],
HB [auth E],
KA [auth H],
LA [auth H],
MB [auth F],
NB [auth F],
OB [auth F],
P [auth A],
Q [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
Y [auth B]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
MG
Query on MG

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EB [auth E],
IA [auth H],
JB [auth F],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
CA [auth G]
K [auth A]
R [auth A]
W [auth B]
X [auth B]
CA [auth G],
K [auth A],
R [auth A],
W [auth B],
X [auth B],
XA [auth D]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.12α = 100.61
b = 81.673β = 97.13
c = 121.377γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2008 390540038

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description