5D4U | pdb_00005d4u

SAM-bound HcgC from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb5D4U/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-09 Released: 2016-07-20 
• Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.
• Funding Organization(s): JST-PRESTO, Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis.

Fujishiro, T., Bai, L., Xu, T., Xie, X., Schick, M., Kahnt, J., Rother, M., Hu, X., Ermler, U., Shima, S.

(2016) Angew Chem Int Ed Engl 55: 9648-9651

• PubMed: 27391308 
• DOI: https://doi.org/10.1002/anie.201604352
• Primary Citation Related Structures: 
  5D4T, 5D4U, 5D4V, 5D5O, 5D5T


• PubMed Abstract: 
  

  Previous retrosynthetic and isotope-labeling studies have indicated that biosynthesis of the iron guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase requires a methyltransferase. This hypothetical enzyme covalently attaches the methyl group at the 3-position of the pyridinol ring. We describe the identification of HcgC, a gene product of the hcgA-G cluster responsible for FeGP cofactor biosynthesis. It acts as an S-adenosylmethionine (SAM)-dependent methyltransferase, based on the crystal structures of HcgC and the HcgC/SAM and HcgC/S-adenosylhomocysteine (SAH) complexes. The pyridinol substrate, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol, was predicted based on properties of the conserved binding pocket and substrate docking simulations. For verification, the assumed substrate was synthesized and used in a kinetic assay. Mass spectrometry and NMR analysis revealed 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol as the reaction product, which confirmed the function of HcgC.

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Organizational Affiliation: 
• Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.
Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-ohkubo 255, Sakura-ku, Saitama, 338-8570, Japan.
Institute of Chemical Science and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland.
Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße, 35032, Marburg, Germany.
Institut für Mikrobiologie, Technische Universität Dresden, 01062, Dresden, Germany.
Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438, Frankfurt/Main, Germany.
Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany. [e-mail].
PRESTO, Japan, Science and Technology Agency, JST, Saitama, 332-0012, Japan. [e-mail].

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 125.4 kDa 
• Atom Count: 8,930 
• Modeled Residue Count: 1,028 
• Deposited Residue Count: 1,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ0489	A, B, C, D	268	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: MJ0489 EC: 2.1.1.400
UniProt
Find proteins for Q57913 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57913  Go to UniProtKB:  Q57913

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A], I [auth B], P [auth C], T [auth D]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SO4	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.29	α = 90
b = 70.52	β = 105.21
c = 91.23	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

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Funding Organization	Location	Grant Number
JST-PRESTO	Japan	--
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description