4YT4

Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: other
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This is version 1.2 of the entry. See complete history


Literature

Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs.

Fujishiro, T.Ataka, K.Ermler, U.Shima, S.

(2015) FEBS J 282: 3412-3423

  • DOI: https://doi.org/10.1111/febs.13351
  • Primary Citation of Related Structures:  
    4YT2, 4YT4, 4YT5, 4YT8

  • PubMed Abstract: 

    [Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4MPT(+)). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4MPT(+) compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. Structural data are available in the Protein Data Bank under the accession numbers 4YT8; 4YT2; 4YT4 and 4YT5.


  • Organizational Affiliation

    Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338375Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ1338
UniProt
Find proteins for Q58734 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58734 
Go to UniProtKB:  Q58734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58734
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE9
Query on FE9

Download Ideal Coordinates CCD File 
B [auth A]iron-guanylyl pyridinol cofactor
C21 H23 Fe N6 O13 P S
AEHOAZNVUAGELD-VPXBKTNXSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.81α = 90
b = 59.81β = 90
c = 183.43γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST-PRESTOJapan--
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description