7O1P

[FeFe]-hydrogenase maturase HydE from T. Maritima (C-ter stretch absent)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B.

Rohac, R.Martin, L.Liu, L.Basu, D.Tao, L.Britt, R.D.Rauchfuss, T.B.Nicolet, Y.

(2021) J Am Chem Soc 143: 8499-8508

  • DOI: https://doi.org/10.1021/jacs.1c03367
  • Primary Citation of Related Structures:  
    7O1O, 7O1P, 7O1S, 7O1T, 7O25, 7O26

  • PubMed Abstract: 

    [FeFe]-hydrogenases use a unique organometallic complex, termed the H cluster, to reversibly convert H 2 into protons and low-potential electrons. It can be best described as a [Fe 4 S 4 ] cluster coupled to a unique [2Fe] H center where the reaction actually takes place. The latter corresponds to two iron atoms, each of which is bound by one CN - ligand and one CO ligand. The two iron atoms are connected by a unique azadithiolate molecule ( - S-CH 2 -NH-CH 2 -S - ) and an additional bridging CO. This [2Fe] H center is built stepwise thanks to the well-orchestrated action of maturating enzymes that belong to the Hyd machinery. Among them, HydG converts l-tyrosine into CO and CN - to produce a unique l-cysteine-Fe(CO) 2 CN species termed complex-B. Very recently, HydE was shown to perform radical-based chemistry using synthetic complex-B as a substrate. Here we report the high-resolution crystal structure that establishes the identity of the complex-B-bound HydE. By triggering the reaction prior to crystallization, we trapped a new five-coordinate Fe species, supporting the proposal that HydE performs complex modifications of complex-B to produce a monomeric "SFe(CO) 2 CN" precursor to the [2Fe] H center. Substrate access, product release, and intermediate transfer are also discussed.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[FeFe] hydrogenase maturase subunit HydE347Thermotoga maritima MSB8Mutation(s): 0 
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

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

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
I [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL
Query on CL

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J [auth A],
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.45α = 90
b = 79.16β = 90
c = 85.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1R35GM126961
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesGM-61153

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description