7YZM | pdb_00007yzm

MgADPNP-bound DCCP:DCCP-R complex

PDB DOI: https://doi.org/10.2210/pdb7YZM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-21 Released: 2022-12-28
Deposition Author(s): Jeoung, J.-H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

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

PubMed: 35905315 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2203576119
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 306.89 kDa
Atom Count: 24,539
Modeled Residue Count: 2,657
Deposited Residue Count: 2,660
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydratase family protein	A, B, E [auth C], F [auth D]	422	Carboxydothermus hydrogenoformans Z-2901	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AET9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative CoA-substrate-specific enzyme activase	C [auth G], D [auth H], G [auth E], H [auth F]	243	Carboxydothermus hydrogenoformans Z-2901	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AET8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BJ8 (Subject of Investigation/LOI) Query on BJ8 Download:Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain S [auth B] SDF format, chain MA [auth C] SDF format, chain I [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain I [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain I [auth A]	I [auth A], MA [auth C], S [auth B], VA [auth D]	Double cubane cluster Fe₈ S₉ CSVVAMDLRWBOEA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain MA [auth C] Focus chain S [auth B] Focus chain VA [auth D] Interactions & Density Focus chain I [auth A] Focus chain MA [auth C] Focus chain S [auth B] Focus chain VA [auth D]
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain KB [auth F] SDF format, chain JA [auth H] SDF format, chain FB [auth E] SDF format, chain AA [auth G] MOL2 format, chain KB [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain FB [auth E] MOL2 format, chain AA [auth G] mmCIF format, chain KB [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain FB [auth E] mmCIF format, chain AA [auth G]	AA [auth G], FB [auth E], JA [auth H], KB [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain FB [auth E] Focus chain JA [auth H] Focus chain KB [auth F] Interactions & Density Focus chain AA [auth G] Focus chain FB [auth E] Focus chain JA [auth H] Focus chain KB [auth F]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth H] SDF format, chain DB [auth E] MOL2 format, chain HA [auth H] MOL2 format, chain DB [auth E] mmCIF format, chain HA [auth H] mmCIF format, chain DB [auth E]	DB [auth E], HA [auth H]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain DB [auth E] Focus chain HA [auth H] Interactions & Density Focus chain DB [auth E] Focus chain HA [auth H]
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain CB [auth D] MOL2 format, chain V [auth B] MOL2 format, chain CB [auth D] mmCIF format, chain V [auth B] mmCIF format, chain CB [auth D]	CB [auth D], V [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain CB [auth D] Focus chain V [auth B] Interactions & Density Focus chain CB [auth D] Focus chain V [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain RA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain RA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], RA [auth C], ZA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth C] Focus chain ZA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain WA [auth D] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain QA [auth C] SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain NA [auth C] SDF format, chain M [auth A] SDF format, chain LB [auth F] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain IB [auth F] SDF format, chain GB [auth E] SDF format, chain BA [auth G] MOL2 format, chain YA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth F] MOL2 format, chain GB [auth E] MOL2 format, chain BA [auth G] mmCIF format, chain YA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth F] mmCIF format, chain GB [auth E] mmCIF format, chain BA [auth G]	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		Interactions Focus chain BA [auth G] Focus chain GB [auth E] Focus chain IB [auth F] Focus chain J [auth A] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain WA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain BA [auth G] Focus chain GB [auth E] Focus chain IB [auth F] Focus chain J [auth A] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain T [auth B] Focus chain U [auth B] Focus chain WA [auth D] Focus chain YA [auth D]
BU3 Query on BU3 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain OB [auth F] SDF format, chain NB [auth F] SDF format, chain MB [auth F] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain HB [auth E] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain BB [auth D] SDF format, chain AB [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain HB [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain BB [auth D] MOL2 format, chain AB [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain NB [auth F] mmCIF format, chain MB [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain HB [auth E] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain BB [auth D] mmCIF format, chain AB [auth D]	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		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HB [auth E] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HB [auth E] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain Y [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain JB [auth F] SDF format, chain IA [auth H] SDF format, chain EB [auth E] MOL2 format, chain Z [auth G] MOL2 format, chain JB [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain EB [auth E] mmCIF format, chain Z [auth G] mmCIF format, chain JB [auth F] mmCIF format, chain IA [auth H] mmCIF format, chain EB [auth E]	EB [auth E], IA [auth H], JB [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EB [auth E] Focus chain IA [auth H] Focus chain JB [auth F] Focus chain Z [auth G] Interactions & Density Focus chain EB [auth E] Focus chain IA [auth H] Focus chain JB [auth F] Focus chain Z [auth G]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain R [auth A] SDF format, chain K [auth A] SDF format, chain CA [auth G] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain R [auth A] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth G] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain R [auth A] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth G]	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		Interactions Focus chain CA [auth G] Focus chain K [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Interactions & Density Focus chain CA [auth G] Focus chain K [auth A] Focus chain R [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D]