6HUZ | pdb_00006huz

HmdII from Desulfurobacterium thermolithotrophum reconstituted with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form B

• PDB DOI: https://doi.org/10.2210/pdb6HUZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfurobacterium thermolithotrophum DSM 11699
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-09 Released: 2019-01-09 
• Deposition Author(s): Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S.
• Funding Organization(s): Max Planck Society, Ministry of Education (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 30600878 
• DOI: https://doi.org/10.1002/anie.201813465
• Primary Citation 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.

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Organizational Affiliation: 
• Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany.
Current address: Microbial Metabolism group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
Mass Spectrometry and Proteomics Unit, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany.
Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
Department of Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438, Frankfurt/Main, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.45 kDa 
• Atom Count: 3,134 
• Modeled Residue Count: 354 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein	A	370	Desulfurobacterium thermolithotrophum DSM 11699	Mutation(s): 0  Gene Names: Dester_1504
UniProt
Find proteins for F0S2B6 (Desulfurobacterium thermolithotrophum (strain DSM 11699 / BSA)) Explore F0S2B6  Go to UniProtKB:  F0S2B6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE9	B [auth A]	iron-guanylyl pyridinol cofactor C21 H23 Fe N6 O13 P S AEHOAZNVUAGELD-VPXBKTNXSA-K
GUE	C [auth A]	5,10-Methenyltetrahydrofolate C20 H22 N7 O6 MEANFMOQMXYMCT-OLZOCXBDSA-O
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.2	α = 90
b = 132.02	β = 90
c = 49.16	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Watanabe, T., Wagner, T., Huang, G., Kahnt, J., Ataka, K., Ermler, U., Shima, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
Ministry of Education (China)	China	--

Revision History  

• 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