5D4T

SeMet-labelled HcgC from Methanocaldococcus jannaschii in space group P212121

PDB DOI: https://doi.org/10.2210/pdb5D4T/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.259
R-Value Work: 0.228
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/anie.201604352
Primary Citation of 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.

Organizational Affiliation

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 246.78 kDa
Atom Count: 15,781
Modelled Residue Count: 1,954
Deposited Residue Count: 2,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ0489	A, B, C, D, E A, B, C, D, E, F, G, H	268	Methanocaldococcus jannaschii	Mutation(s): 0 Gene Names: MJ0489
UniProt
Find proteins for Q57913 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57913 Go to UniProtKB: Q57913
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.259
R-Value Work: 0.228
R-Value Observed: 0.229
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.43	α = 90
b = 145	β = 90
c = 150.55	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
XDS	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2016-08-10
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.