7NP8 | pdb_00007np8

Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanocaldococcus jannaschii at 2.3-A resolution

PDB DOI: https://doi.org/10.2210/pdb7NP8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Mutation(s): No

Deposited: 2021-02-26 Released: 2022-03-23
Deposition Author(s): Jespersen, M., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.

Jespersen, M., Pierik, A.J., Wagner, T.

(2023) Nat Chem Biol

PubMed: 36658338 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-022-01232-y
Primary Citation Related Structures:
7NP8, 7NPA

PubMed Abstract:
Methanogenic archaea are main actors in the carbon cycle but are sensitive to reactive sulfite. Some methanogens use a sulfite detoxification system that combines an F ₄₂₀H ₂-oxidase with a sulfite reductase, both of which are proposed precursors of modern enzymes. Here, we present snapshots of this coupled system, named coenzyme F ₄₂₀-dependent sulfite reductase (Group I Fsr), obtained from two marine methanogens. Fsr organizes as a homotetramer, harboring an intertwined six-[4Fe-4S] cluster relay characterized by spectroscopy. The wire, spanning 5.4 nm, electronically connects the flavin to the siroheme center. Despite a structural architecture similar to dissimilatory sulfite reductases, Fsr shows a siroheme coordination and a reaction mechanism identical to assimilatory sulfite reductases. Accordingly, the reaction of Fsr is unidirectional, reducing sulfite or nitrite with F ₄₂₀H ₂. Our results provide structural insights into this unique fusion, in which a primitive sulfite reductase turns a poison into an elementary block of life.

Organizational Affiliation

Max Planck Institute for Marine Microbiology, Bremen, Germany.

Macromolecule Content

Total Structure Weight: 299.34 kDa
Atom Count: 21,246
Modeled Residue Count: 2,478
Deposited Residue Count: 2,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420-dependent sulfite reductase	A, B, C, D	620	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 EC: 1.8.98.3
UniProt
Find proteins for Q58280 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58280 Go to UniProtKB: Q58280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58280
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRM (Subject of Investigation/LOI) Query on SRM Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth A] SDF format, chain VB [auth D] SDF format, chain YA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain YA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain VB [auth D] mmCIF format, chain YA [auth C]	EA [auth B], M [auth A], VB [auth D], YA [auth C]	SIROHEME C₄₂ H₄₄ Fe N₄ O₁₆ DLKSSIHHLYNIKN-MWBYXLBFSA-L		Interactions Focus chain EA [auth B] Focus chain M [auth A] Focus chain VB [auth D] Focus chain YA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain M [auth A] Focus chain VB [auth D] Focus chain YA [auth C]
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain J [auth A] SDF format, chain SB [auth D] SDF format, chain XA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain XA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain SB [auth D] mmCIF format, chain XA [auth C]	CA [auth B], J [auth A], SB [auth D], XA [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth B] Focus chain J [auth A] Focus chain SB [auth D] Focus chain XA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain J [auth A] Focus chain SB [auth D] Focus chain XA [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain NB [auth D] SDF format, chain OB [auth D] SDF format, chain PB [auth D] SDF format, chain QB [auth D] SDF format, chain RA [auth C] SDF format, chain RB [auth D] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain SA [auth C] SDF format, chain H [auth A] SDF format, chain DA [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain OB [auth D] MOL2 format, chain PB [auth D] MOL2 format, chain QB [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain OB [auth D] mmCIF format, chain PB [auth D] mmCIF format, chain QB [auth D] mmCIF format, chain RA [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] DA [auth B] E [auth A] F [auth A] AA [auth B], BA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth A], NB [auth D], OB [auth D], PB [auth D], QB [auth D], RA [auth C], RB [auth D], SA [auth C], TA [auth C], TB [auth D], UA [auth C], VA [auth C], WA [auth C], X [auth B], Y [auth B], Z [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain NB [auth D] Focus chain OB [auth D] Focus chain PB [auth D] Focus chain QB [auth D] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain GA [auth B] SDF format, chain P [auth A] SDF format, chain ZB [auth D] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain ZB [auth D] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain ZB [auth D]	CB [auth C], DB [auth C], GA [auth B], P [auth A], ZB [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain GA [auth B] Focus chain P [auth A] Focus chain ZB [auth D] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain GA [auth B] Focus chain P [auth A] Focus chain ZB [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain DC [auth D] SDF format, chain EC [auth D] SDF format, chain FA [auth B] SDF format, chain FC [auth D] SDF format, chain GC [auth D] SDF format, chain HC [auth D] SDF format, chain IB [auth C] SDF format, chain IC [auth D] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain KC [auth D] SDF format, chain LA [auth B] SDF format, chain LC [auth D] SDF format, chain MA [auth B] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain WB [auth D] SDF format, chain XB [auth D] SDF format, chain YB [auth D] SDF format, chain ZA [auth C] SDF format, chain O [auth A] SDF format, chain JC [auth D] SDF format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain DC [auth D] MOL2 format, chain EC [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain GC [auth D] MOL2 format, chain HC [auth D] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain LC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain WB [auth D] MOL2 format, chain XB [auth D] MOL2 format, chain YB [auth D] MOL2 format, chain ZA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain DC [auth D] mmCIF format, chain EC [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FC [auth D] mmCIF format, chain GC [auth D] mmCIF format, chain HC [auth D] mmCIF format, chain IB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain LC [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MC [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain WB [auth D] mmCIF format, chain XB [auth D] mmCIF format, chain YB [auth D] mmCIF format, chain ZA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain JC [auth D] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] DC [auth D] EC [auth D] FA [auth B] AB [auth C], BB [auth C], DC [auth D], EC [auth D], FA [auth B], FC [auth D], GC [auth D], HC [auth D], IB [auth C], IC [auth D], JB [auth C], JC [auth D], KA [auth B], KB [auth C], KC [auth D], LA [auth B], LC [auth D], MA [auth B], MC [auth D], N [auth A], NA [auth B], O [auth A], OA [auth B], PA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], WB [auth D], XB [auth D], YB [auth D], ZA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain HC [auth D] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain LA [auth B] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YB [auth D] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain DC [auth D] Focus chain EC [auth D] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain HC [auth D] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain LA [auth B] Focus chain LC [auth D] Focus chain MA [auth B] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain WB [auth D] Focus chain XB [auth D] Focus chain YB [auth D] Focus chain ZA [auth C]
SO3 (Subject of Investigation/LOI) Query on SO3 Download:Ideal Coordinates CCD File SDF format, chain HB [auth C] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain UB [auth D] MOL2 format, chain HB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain UB [auth D] mmCIF format, chain HB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain UB [auth D]	HB [auth C], JA [auth B], L [auth A], UB [auth D]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain HB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain UB [auth D] Interactions & Density Focus chain HB [auth C] Focus chain JA [auth B] Focus chain L [auth A] Focus chain UB [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain NC [auth D] MOL2 format, chain NC [auth D] mmCIF format, chain NC [auth D]	NC [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain NC [auth D] Interactions & Density Focus chain NC [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain CC [auth D] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain GB [auth C] SDF format, chain IA [auth B] SDF format, chain Q [auth A] SDF format, chain HA [auth B] SDF format, chain AC [auth D] MOL2 format, chain BC [auth D] MOL2 format, chain CC [auth D] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain AC [auth D] mmCIF format, chain BC [auth D] mmCIF format, chain CC [auth D] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain AC [auth D]	AC [auth D] BC [auth D] CC [auth D] EB [auth C] FB [auth C] AC [auth D], BC [auth D], CC [auth D], EB [auth C], FB [auth C], GB [auth C], HA [auth B], IA [auth B], Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain AC [auth D] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain LB [auth C] SDF format, chain MB [auth C] SDF format, chain OC [auth D] SDF format, chain QA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] mmCIF format, chain LB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain OC [auth D] mmCIF format, chain QA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A]	LB [auth C] MB [auth C] OC [auth D] QA [auth B] V [auth A] LB [auth C], MB [auth C], OC [auth D], QA [auth B], V [auth A], W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain LB [auth C] Focus chain MB [auth C] Focus chain OC [auth D] Focus chain QA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain LB [auth C] Focus chain MB [auth C] Focus chain OC [auth D] Focus chain QA [auth B] Focus chain V [auth A] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.258	α = 90
b = 172.202	β = 90
c = 195.888	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Jespersen, M.

Wagner, T.

Funding Organization	Location	Grant Number
Max Planck Society	Germany	/
German Research Foundation (DFG)	Germany	Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2023-04-05
Changes: Database references
Version 2.0: 2023-12-06
Changes: Data collection, Non-polymer description, Structure summary