7WH0 | pdb_00007wh0

structure of C elegans BCMO-1

• PDB DOI: https://doi.org/10.2210/pdb7WH0/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-29 Released: 2022-02-02 
• Deposition Author(s): Pan, W., Liu, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Analysis of Nonheme Iron Enzymes BCMO-1 and BCMO-2 from Caenorhabditis elegans .

Pan, W., Zhou, Y.L., Wang, J., Dai, H.E., Wang, X., Liu, L.

(2022) Front Mol Biosci 9: 844453-844453

• PubMed: 35223999 
• DOI: https://doi.org/10.3389/fmolb.2022.844453
• Primary Citation Related Structures: 
  7WH0, 7WH1


• PubMed Abstract: 
  

  Carotenoid metabolism is critical for diverse physiological processes. The nematode Caenorhabditis elegans has two genes that are annotated as β-carotene 15,15'-monooxygenase (BCMO) and are 17 centimorgan apart on chromosome II, but the function of BCMO-1 and BCMO-2 remains uncharacterized. Sequence homology indicates that the two enzymes belong to the carotenoid cleavage dioxygenase family that share a seven-bladed β-propeller fold with a nonheme iron center. Here we determined crystal structures of BCMO-1 and BCMO-2 at resolutions of 1.8 and 1.9 Å, respectively. Structural analysis reveals that BCMO-1 and BCMO-2 are strikingly similar to each other. We also characterized their β-carotene cleavage activity, but the results suggest that they may not act as β-carotene 15,15'-oxygenases.

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Organizational Affiliation: 
• School of Life Sciences, Anhui University, Hefei, China.
Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 126.06 kDa 
• Atom Count: 9,472 
• Modeled Residue Count: 1,058 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Carotene 15,15'-MonoOxygenase	A, B	549	Caenorhabditis elegans	Mutation(s): 0  Gene Names: bcmo-1
UniProt
Find proteins for Q9U2E4 (Caenorhabditis elegans) Explore Q9U2E4  Go to UniProtKB:  Q9U2E4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXD (Subject of Investigation/LOI)	E [auth A], H [auth B]	OXALIC ACID C2 H2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)	C [auth A], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.204	α = 90
b = 104.733	β = 102.16
c = 76.438	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Pan, W., Liu, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description