5D4V | pdb_00005d4v

HcgC with SAH and a guanylylpyridinol (GP) derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YGPClick on this verticalbar to view detailsBest fitted SAHClick on this verticalbar to view details

This is version 1.2 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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MJ0489
A, B, C, D
268Methanocaldococcus jannaschiiMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57913
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YGP
Query on YGP

Download Ideal Coordinates CCD File 
O [auth B],
W [auth C]
5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine
C17 H21 N6 O9 P
SHYVQHDJQQBUQP-UBEDBUPSSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
P [auth C],
X [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.11α = 90
b = 70.48β = 105.19
c = 91.77γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YGPClick on this verticalbar to view detailsBest fitted SAHClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


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

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
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description