3F46 | pdb_00003f46

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.

Hiromoto, T.Ataka, K.Pilak, O.Vogt, S.Stagni, M.S.Meyer-Klaucke, W.Warkentin, E.Thauer, R.K.Shima, S.Ermler, U.

(2009) FEBS Lett 583: 585-590

  • DOI: https://doi.org/10.1016/j.febslet.2009.01.017
  • Primary Citation Related Structures: 
    3F46, 3F47

  • PubMed Abstract: 

    [Fe]-hydrogenase is one of three types of enzymes known to activate H(2). Crystal structure analysis recently revealed that its active site iron is ligated square-pyramidally by Cys176-sulfur, two CO, an "unknown" ligand and the sp(2)-hybridized nitrogen of a unique iron-guanylylpyridinol-cofactor. We report here on the structure of the C176A mutated enzyme crystallized in the presence of dithiothreitol (DTT). It suggests an iron center octahedrally coordinated by one DTT-sulfur and one DTT-oxygen, two CO, the 2-pyridinol's nitrogen and the 2-pyridinol's 6-formylmethyl group in an acyl-iron ligation. This result led to a re-interpretation of the iron ligation in the wild-type.


  • Organizational Affiliation
    • Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 39.5 kDa 
  • Atom Count: 2,887 
  • Modeled Residue Count: 345 
  • Deposited Residue Count: 358 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5,10-methenyltetrahydromethanopterin hydrogenase358Methanocaldococcus jannaschiiMutation(s): 1 
Gene Names: hmdMJ0784
EC: 1.12.98.2
UniProt
Find proteins for Q58194 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58194 
Go to UniProtKB:  Q58194
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58194
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I2C

Query on I2C



Download:Ideal Coordinates CCD File
B [auth A]5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine
C19 H23 N6 O10 P
FVDPDULUWMBTHF-IPKTUIKJSA-N
DTV

Query on DTV



Download:Ideal Coordinates CCD File
F [auth A](2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CMO

Query on CMO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.35α = 90
b = 96.35β = 90
c = 166.61γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description