8QMK

Enzymatically-produced complex-B bound TmHydE structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the ( kappa 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE.

Omeiri, J.Martin, L.Usclat, A.Cherrier, M.V.Nicolet, Y.

(2023) Angew Chem Int Ed Engl 62: e202314819-e202314819

  • DOI: https://doi.org/10.1002/anie.202314819
  • Primary Citation of Related Structures:  
    8QMK, 8QML, 8QMM, 8QMN

  • PubMed Abstract: 

    [FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe 4 S 4 ] center with a binuclear iron center ([2Fe] H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe] H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.


  • Organizational Affiliation

    Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[FeFe] hydrogenase maturase subunit HydE358Thermotoga maritima MSB8Mutation(s): 4 
Gene Names: TM_1269THEMA_07990Tmari_1274
EC: 1.8
UniProt
Find proteins for Q9X0Z6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0Z6 
Go to UniProtKB:  Q9X0Z6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0Z6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download Ideal Coordinates CCD File 
F [auth A]3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
SAH
Query on SAH

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H [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SF4
Query on SF4

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G [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CYS
Query on CYS

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L [auth A]CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
SO4
Query on SO4

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K [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE2 (Subject of Investigation/LOI)
Query on FE2

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B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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I [auth A],
J [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO (Subject of Investigation/LOI)
Query on CMO

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C [auth A],
D [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
CYN (Subject of Investigation/LOI)
Query on CYN

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E [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.83α = 90
b = 83.56β = 90
c = 70.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
Agence Nationale de la Recherche (ANR)FranceANR-17-EURE-0003

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Database references
  • Version 1.3: 2023-12-27
    Changes: Database references