6M25

Sirohydrochlorin nickelochelatase CfbA in P41 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis.

Fujishiro, T.Ogawa, S.

(2021) Chem Sci 12: 2172-2180

  • DOI: https://doi.org/10.1039/d0sc05439a
  • Primary Citation of Related Structures:  
    6M25, 6M26, 6M27, 6M28, 6M29, 6M2A, 6M2E, 6M2F, 6M2G, 6M2H

  • PubMed Abstract: 

    The class II chelatase CfbA catalyzes Ni 2+ insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatase in vitro . Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni 2+ and Co 2+ remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures of Methanocaldococcus jannaschii wild-type CfbA with various ligands, including SHC, Ni 2+ , Ni-SHC, and Co 2+ were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni 2+ -SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co 2+ than Ni 2+ . Meanwhile, an in vitro activity assay confirmed the different reaction rates for Ni 2+ and Co 2+ by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni 2+ insertion catalytic mechanism was proposed: Ni 2+ insertion to SHC is promoted by the support of an acetate side chain of SHC.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Shimo-Okubo 255 Sakura Saitama 338-8570 Japan tfujishiro@mail.saitama-u.ac.jp +81-48-858-9293.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sirohydrochlorin cobaltochelatase
A, B
143Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: cbiXcfbAMJ0970
EC: 4.99.1.3 (PDB Primary Data), 4.99.1.11 (PDB Primary Data)
UniProt
Find proteins for Q58380 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58380 
Go to UniProtKB:  Q58380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58380
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.55α = 90
b = 68.55β = 90
c = 82.41γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H04639

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description