6QFV

Human carbonic anhydrase II with bound IrCp* complex (cofactor 8) to generate an artificial transfer hydrogenase (ATHase)

• PDB DOI: https://doi.org/10.2210/pdb6QFV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-10 Released: 2019-04-17 
• Deposition Author(s): Rebelein, J.G.
• Funding Organization(s): Swiss National Science Foundation, European Research Council, European Molecular Biology Organization

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Chemical Optimization of Whole-Cell Transfer Hydrogenation Using Carbonic Anhydrase as Host Protein.

Rebelein, J.G., Cotelle, Y., Garabedian, B., Ward, T.R.

(2019) ACS Catal 9: 4173-4178

• PubMed: 31080690 
• DOI: https://doi.org/10.1021/acscatal.9b01006
• Primary Citation of Related Structures:  
  6QFU, 6QFV, 6QFW, 6QFX


• PubMed Abstract: 
  

  Artificial metalloenzymes combine a synthetic metallocofactor with a protein scaffold and can catalyze abiotic reactions in vivo . Herein, we report on our efforts to valorize human carbonic anhydrase II as a scaffold for whole-cell transfer hydrogenation. Two platforms were tested: periplasmic compartmentalization and surface display in Escherichia coli . A chemical optimization of an IrCp* cofactor was performed. This led to 90 turnovers in the cell, affording a 69-fold increase in periplasmic product formation over the previously reported, sulfonamide-bearing IrCp* cofactor. These findings highlight the versatility of carbonic anhydrase as a promising scaffold for whole-cell catalysis with artificial metalloenzymes.

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Organizational Affiliation: 

Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 30.2 kDa 
• Atom Count: 2,381 
• Modelled Residue Count: 255 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J0N (Subject of Investigation/LOI)	B [auth A]	4-[2-(9-chloranyl-2',3',4',5',6'-pentamethyl-7-oxidanylidene-spiro[1$l^{4},8-diaza-9$l^{8}-iridabicyclo[4.3.0]nona-1(6),2,4-triene-9,1'-1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane]-8-yl)ethyl]benzenesulfonamide C24 H29 Cl Ir N3 O3 S GPKFYIUARYJGFU-UHFFFAOYSA-L
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.396	α = 90
b = 41.68	β = 104.4
c = 72.353	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Rebelein, J.G.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	200020_162348
European Research Council		DrEAM
Swiss National Science Foundation	Switzerland	NCCR MSE
European Molecular Biology Organization	Germany	ALTF 194-2017

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description