Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 71.64 kDa 
• Atom Count: 4965 
• Modelled Residue Count: 603 
• Deposited Residue Count: 654 
• Unique protein chains: 1

3WV7

HcgE from Methanothermobacter marburgensis

• PDB DOI: 10.2210/pdb3WV7/pdb

• Classification: TRANSFERASE
• Organism(s): Methanothermobacter marburgensis str. Marburg
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-16 Released: 2015-04-29 
• Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

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

• PubMed: 25882909 
• DOI: 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.

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Organizational Affiliation: 

PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, 332-0012 Saitama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hmd co-occurring protein HcgE	A, B, C	218	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  Gene Names: hcgE, MTBMA_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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.39	α = 90
b = 73.52	β = 118.05
c = 68.58	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-16 
• Released Date: 2015-04-29 
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release