7O1T

Fe(CO)2CNCl species bound [HydE from T. Maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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 HydE358Thermotoga maritimaMutation(s): 3 
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 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download Ideal Coordinates CCD File 
I [auth A]3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
5X8
Query on 5X8

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H [auth A]S-adenosyl-L-cysteine
C13 H18 N6 O5 S
RVFHZLGRQFCOKV-MACXSXHHSA-N
SF4
Query on SF4

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

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P [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CYS (Subject of Investigation/LOI)
Query on CYS

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B [auth A]CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
PYR
Query on PYR

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G [auth A]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

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

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

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

Download Ideal Coordinates CCD File 
F [auth A],
O [auth A]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.54α = 90
b = 82.83β = 90
c = 70.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
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: Advisory, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-31
    Changes: Refinement description