7O26

Complex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima (5'dA + Methionine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 5ADClick on this verticalbar to view detailsBest fitted CYSClick on this verticalbar to view details

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 HydE348Thermotoga 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
Expand
  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

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M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
SF4
Query on SF4

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R [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
5AD (Subject of Investigation/LOI)
Query on 5AD

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J [auth A]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
FES
Query on FES

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K [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MET
Query on MET

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G [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
IOD
Query on IOD

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S [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
GOL
Query on GOL

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L [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

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

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T [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S
Query on H2S

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H [auth A],
I [auth A]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
CMO (Subject of Investigation/LOI)
Query on CMO

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

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F [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.88α = 90
b = 79.84β = 90
c = 86.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 5ADClick on this verticalbar to view detailsBest fitted CYSClick on this verticalbar to view details

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