6HUX

HmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates.

Watanabe, T.Wagner, T.Huang, G.Kahnt, J.Ataka, K.Ermler, U.Shima, S.

(2019) Angew Chem Int Ed Engl 58: 3506-3510

  • DOI: https://doi.org/10.1002/anie.201813465
  • Primary Citation of Related Structures:  
    6HUX, 6HUY, 6HUZ

  • PubMed Abstract: 

    [Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H 4 MPT + ) with H 2 . H 4 MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog, termed HmdII, and the HcgA-G proteins. The latter are required for the biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H 4 MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the hydrogenation of derivatives of tetrahydrofolate, the bacterial C1-carrier, albeit with low enzymatic activities. The crystal structures show how Hmd recognizes tetrahydrofolate derivatives. These findings have an impact on future biotechnology by identifying a bacterial Hmd paralog.


  • Organizational Affiliation

    Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, 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 jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1338
EC: 1.12.98.2
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
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E4M
Query on E4M

Download Ideal Coordinates CCD File 
M [auth A]1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol
C31 H44 N6 O16 P
RANKJVUGLXUXOL-CAFBYHECSA-O
FE9
Query on FE9

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K [auth A]iron-guanylyl pyridinol cofactor
C21 H23 Fe N6 O13 P S
AEHOAZNVUAGELD-VPXBKTNXSA-K
SO4
Query on SO4

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O [auth A]
P [auth A]
Q [auth A]
R [auth A]
S [auth A]
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

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V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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Y [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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N [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.281α = 90
b = 124.281β = 90
c = 150.086γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Ministry of Education (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description