7NPA | pdb_00007npa

Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution

• PDB DOI: https://doi.org/10.2210/pdb7NPA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermococcus thermolithotrophicus DSM 2095
• 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: 1.55 Å
• R-Value Free: 
  0.171 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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 
• 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 ₄₂₀ H 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 ₄₂₀ H 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.
Biochemistry, Faculty of Chemistry, University of Kaiserslautern-Landau, Kaiserslautern, Germany.
Max Planck Institute for Marine Microbiology, Bremen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1,184.79 kDa 
• Atom Count: 93,689 
• Modeled Residue Count: 9,878 
• Deposited Residue Count: 9,888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420-dependent sulfite reductase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	618	Methanothermococcus thermolithotrophicus DSM 2095	Mutation(s): 0  EC: 1.8.98.3
UniProt
Find proteins for A0A2Z5PF12 (Methanococcus maripaludis OS7) Explore A0A2Z5PF12  Go to UniProtKB:  A0A2Z5PF12

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRM (Subject of Investigation/LOI)	CM [auth O], GK [auth M], IF [auth G], IG [auth H], NE [auth F], NL [auth N], OJ [auth L], SD [auth E], SI [auth K], VA [auth B], VC [auth D], WH [auth J], Y [auth A], YB [auth C], ZG [auth I], ZM [auth P]	SIROHEME C42 H44 Fe N4 O16 DLKSSIHHLYNIKN-MWBYXLBFSA-L
FAD (Subject of Investigation/LOI)	CL [auth N], DK [auth M], FF [auth G], FG [auth H], KE [auth F], KL [auth N], LJ [auth L], PD [auth E], PI [auth K], SA [auth B], SC [auth D], TH [auth J], V [auth A], VB [auth C], WG [auth I], WM [auth P], ZL [auth O]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4 (Subject of Investigation/LOI)	AF [auth G], AG [auth H], AK [auth M], AM [auth O], BF [auth G], BG [auth H], BK [auth M], CF [auth G], CG [auth H], CK [auth M], DF [auth G], DG [auth H], DL [auth N], EF [auth G], EG [auth H], EK [auth M], EL [auth N], FE [auth F], FL [auth N], GE [auth F], GF [auth G], GG [auth H], GJ [auth L], GL [auth N], HE [auth F], HJ [auth L], HL [auth N], IE [auth F], IJ [auth L], IL [auth N], JE [auth F], JJ [auth L], JL [auth N], KD [auth E], KI [auth K], KJ [auth L], LD [auth E], LE [auth F], LI [auth K], MD [auth E], MI [auth K], MJ [auth L], NA [auth B], NC [auth D], ND [auth E], NI [auth K], OA [auth B], OC [auth D], OD [auth E], OH [auth J], OI [auth K], PA [auth B], PC [auth D], PH [auth J], Q [auth A], QA [auth B], QB [auth C], QC [auth D], QD [auth E], QH [auth J], QI [auth K], R [auth A], RA [auth B], RB [auth C], RC [auth D], RG [auth I], RH [auth J], RM [auth P], S [auth A], SB [auth C], SG [auth I], SH [auth J], SM [auth P], T [auth A], TA [auth B], TB [auth C], TC [auth D], TG [auth I], TM [auth P], U [auth A], UB [auth C], UG [auth I], UH [auth J], UL [auth O], UM [auth P], VG [auth I], VL [auth O], VM [auth P], W [auth A], WB [auth C], WL [auth O], XG [auth I], XL [auth O], XM [auth P], YJ [auth M], YL [auth O], ZJ [auth M]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
TRS	JH [auth I], ZF [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	MC [auth D], MK [auth M], PL [auth N], RK [auth M], YI [auth K]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	BE [auth E], BJ [auth K], CJ [auth K], ED [auth D], FD [auth D], FI [auth J], FN [auth P], GD [auth D], GI [auth J], GN [auth P], HC [auth C], IA [auth A], KB [auth B], KH [auth I], LB [auth B], MG [auth H], MM [auth O], NG [auth H], NM [auth O], RL [auth N], SJ [auth L], TE [auth F], TJ [auth L], UE [auth F], UJ [auth L], VE [auth F], VF [auth G], WE [auth F], WK [auth M], XK [auth M], YK [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AJ [auth K], BC [auth C], BH [auth I], BI [auth J], BN [auth P], CB [auth B], CN [auth P], DB [auth B], EI [auth J], HH [auth I], JB [auth B], JM [auth O], LK [auth M], ML [auth N], PB [auth C], QL [auth N], SE [auth F], SF [auth G], XD [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth A], AB [auth B], AC [auth C], AD [auth D], AE [auth E], AH [auth I], AI [auth J], AN [auth P], BA [auth A], BB [auth B], BD [auth D], BM [auth O], CA [auth A], CC [auth C], CD [auth D], CH [auth I], CI [auth J], DA [auth A], DC [auth C], DD [auth D], DH [auth I], DI [auth J], DM [auth O], DN [auth P], EA [auth A], EB [auth B], EC [auth C], EH [auth I], EM [auth O], EN [auth P], FA [auth A], FB [auth B], FC [auth C], FH [auth I], FK [auth M], FM [auth O], GA [auth A], GB [auth B], GC [auth C], GH [auth I], GM [auth O], HA [auth A], HB [auth B], HF [auth G], HG [auth H], HK [auth M], HM [auth O], IB [auth B], IH [auth I], IK [auth M], IM [auth O], JF [auth G], JG [auth H], JK [auth M], KF [auth G], KG [auth H], KK [auth M], KM [auth O], LF [auth G], LG [auth H], LL [auth N], LM [auth O], MA [auth B], ME [auth F], MF [auth G], NF [auth G], NJ [auth L], NK [auth M], OE [auth F], OF [auth G], OK [auth M], OL [auth N], PE [auth F], PF [auth G], PJ [auth L], PK [auth M], QE [auth F], QF [auth G], QJ [auth L], QK [auth M], RD [auth E], RE [auth F], RF [auth G], RI [auth K], RJ [auth L], SK [auth M], TD [auth E], TF [auth G], TI [auth K], TK [auth M], UA [auth B], UC [auth D], UD [auth E], UF [auth G], UI [auth K], UK [auth M], VD [auth E], VH [auth J], VI [auth K], VK [auth M], WA [auth B], WC [auth D], WD [auth E], WI [auth K], X [auth A], XA [auth B], XB [auth C], XC [auth D], XH [auth J], XI [auth K], YA [auth B], YC [auth D], YD [auth E], YG [auth I], YH [auth J], YM [auth P], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D], ZD [auth E], ZH [auth J], ZI [auth K]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AL [auth M], BL [auth M], DE [auth E], EE [auth E], EJ [auth K], FJ [auth K], ID [auth D], II [auth J], IN [auth P], JC [auth C], JD [auth D], JI [auth J], JN [auth P], KA [auth A], KC [auth C], LA [auth A], MH [auth I], NB [auth B], NH [auth I], OB [auth B], PG [auth H], PM [auth O], QG [auth H], QM [auth O], TL [auth N], WJ [auth L], XF [auth G], YE [auth F], YF [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S (Subject of Investigation/LOI)	CE [auth E], DJ [auth K], HD [auth D], HI [auth J], HN [auth P], IC [auth C], JA [auth A], LH [auth I], MB [auth B], OG [auth H], OM [auth O], SL [auth N], VJ [auth L], WF [auth G], XE [auth F], ZK [auth M]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N
LI	KN [auth P], LC [auth C], XJ [auth L], ZE [auth F]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.171 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.148	α = 102.28
b = 124.157	β = 95.71
c = 241.062	γ = 90.25

Software Package:

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

Structure Validation

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  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references, Refinement description
• Version 2.0: 2023-12-06
  Changes: Data collection, Non-polymer description, Structure summary
• Version 2.1: 2024-02-07
  Changes: Refinement description