5UJC | pdb_00005ujc

Crystal structure of a C.elegans B12-trafficking protein CblC, a human MMACHC homologue

• PDB DOI: https://doi.org/10.2210/pdb5UJC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-01-17 Released: 2017-05-03 
• Deposition Author(s): Li, Z., Shanmuganathan, A., Ruetz, M., Yamada, K., Lesniak, N.A., Krautler, B., Brunold, T.C., Banerjee, R., Koutmos, M.
• Funding Organization(s): American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Coordination chemistry controls the thiol oxidase activity of the B12-trafficking protein CblC.

Li, Z., Shanmuganathan, A., Ruetz, M., Yamada, K., Lesniak, N.A., Krautler, B., Brunold, T.C., Koutmos, M., Banerjee, R.

(2017) J Biological Chem 292: 9733-9744

• PubMed: 28442570 
• DOI: https://doi.org/10.1074/jbc.M117.788554
• Primary Citation Related Structures: 
  5UJC


• PubMed Abstract: 
  

  The cobalamin or B ₁₂ cofactor supports sulfur and one-carbon metabolism and the catabolism of odd-chain fatty acids, branched-chain amino acids, and cholesterol. CblC is a B ₁₂ -processing enzyme involved in an early cytoplasmic step in the cofactor-trafficking pathway. It catalyzes the glutathione (GSH)-dependent dealkylation of alkylcobalamins and the reductive decyanation of cyanocobalamin. CblC from Caenorhabditis elegans ( ce CblC) also exhibits a robust thiol oxidase activity, converting reduced GSH to oxidized GSSG with concomitant scrubbing of ambient dissolved O ₂ The mechanism of thiol oxidation catalyzed by ce CblC is not known. In this study, we demonstrate that novel coordination chemistry accessible to ce CblC-bound cobalamin supports its thiol oxidase activity via a glutathionyl-cobalamin intermediate. Deglutathionylation of glutathionyl-cobalamin by a second molecule of GSH yields GSSG. The crystal structure of ce CblC provides insights into how architectural differences at the α- and β-faces of cobalamin promote the thiol oxidase activity of ce CblC but mute it in wild-type human CblC. The R161G and R161Q mutations in human CblC unmask its latent thiol oxidase activity and are correlated with increased cellular oxidative stress disease. In summary, we have uncovered key architectural features in the cobalamin-binding pocket that support unusual cob(II)alamin coordination chemistry and enable the thiol oxidase activity of ce CblC.

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Organizational Affiliation: 
• From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600.
the Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814.
the Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria, and.
the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706.
From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, [e-mail].

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.24 kDa 
• Atom Count: 2,654 
• Modeled Residue Count: 267 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MMACHC-like protein	A	270	Caenorhabditis elegans	Mutation(s): 0  Gene Names: cblc-1, ZK546.17 EC: 1.16.1
UniProt
Find proteins for Q7Z144 (Caenorhabditis elegans) Explore Q7Z144  Go to UniProtKB:  Q7Z144

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COB	B [auth A]	CO-METHYLCOBALAMIN C63 H91 Co N13 O14 P BMOGZGJBQIUQJG-BYLSPCLQSA-N
TAR	E [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
TLA	C [auth A], D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.008	α = 90
b = 66.089	β = 90
c = 92.826	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Li, Z., Shanmuganathan, A., Ruetz, M., Yamada, K., Lesniak, N.A., Krautler, B., Brunold, T.C., Banerjee, R., Koutmos, M.

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Funding Organization	Location	Grant Number
American Heart Association	United States	13SDG14560056

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description