3WV9

Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobacter marburgensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor

Fujishiro, T.Kahnt, J.Ermler, U.Shima, S.

(2015) Nat Commun 6: 6895-6895

  • DOI: https://doi.org/10.1038/ncomms7895
  • Primary Citation of Related Structures:  
    3WV7, 3WV8, 3WV9, 3WVA, 3WVB, 3WVC

  • PubMed Abstract: 

    The iron-guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase contains a prominent iron centre with an acyl-Fe bond and is the only acyl-organometallic iron compound found in nature. Here, we identify the functions of HcgE and HcgF, involved in the biosynthesis of the FeGP cofactor using structure-to-function strategy. Analysis of the HcgE and HcgF crystal structures with and without bound substrates suggest that HcgE catalyses the adenylylation of the carboxy group of guanylylpyridinol (GP) to afford AMP-GP, and subsequently HcgF catalyses the transesterification of AMP-GP to afford a Cys (HcgF)-S-GP thioester. Both enzymatic reactions are confirmed by in vitro assays. The structural data also offer plausible catalytic mechanisms. This strategy of thioester activation corresponds to that used for ubiquitin activation, a key event in the regulation of multiple cellular processes. It further implicates a nucleophilic attack onto the acyl carbon presumably via an electron-rich Fe(0)- or Fe(I)-carbonyl complex in the Fe-acyl formation.


  • Organizational Affiliation

    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
Hmd co-occurring protein HcgE
A, B, C, D
218Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: hcgEMTBMA_c15310
EC: 2.7.7
UniProt
Find proteins for D9PY12 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg))
Explore D9PY12 
Go to UniProtKB:  D9PY12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9PY12
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FEG
Query on FEG

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
N [auth C]
5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine
C19 H23 N6 O11 P
GTHOTKPHMGEHFD-ACDAHVMNSA-N
ATP
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
M [auth C],
S [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85α = 90
b = 85β = 90
c = 120.78γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description