7WWF | pdb_00007wwf

Crystal structure of BioH3 from Mycolicibacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb7WWF/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-12 Released: 2022-07-06
Deposition Author(s): Yang, J., Xu, Y.C., Gan, J.H., Feng, Y.J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.189 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target.

Xu, Y., Yang, J., Li, W., Song, S., Shi, Y., Wu, L., Sun, J., Hou, M., Wang, J., Jia, X., Zhang, H., Huang, M., Lu, T., Gan, J., Feng, Y.

(2022) PLoS Pathog 18: e1010615-e1010615

PubMed: 35816546 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1010615
Primary Citation Related Structures:
7WWF

PubMed Abstract:
Tuberculosis (TB) is one of the leading infectious diseases of global concern, and one quarter of the world's population are TB carriers. Biotin metabolism appears to be an attractive anti-TB drug target. However, the first-stage of mycobacterial biotin synthesis is fragmentarily understood. Here we report that three evolutionarily-distinct BioH isoenzymes (BioH1 to BioH3) are programmed in biotin synthesis of Mycobacterium smegmatis. Expression of an individual bioH isoform is sufficient to allow the growth of an Escherichia coli ΔbioH mutant on the non-permissive condition lacking biotin. The enzymatic activity in vitro combined with biotin bioassay in vivo reveals that BioH2 and BioH3 are capable of removing methyl moiety from pimeloyl-ACP methyl ester to give pimeloyl-ACP, a cognate precursor for biotin synthesis. In particular, we determine the crystal structure of dimeric BioH3 at 2.27Å, featuring a unique lid domain. Apart from its catalytic triad, we also dissect the substrate recognition of BioH3 by pimeloyl-ACP methyl ester. The removal of triple bioH isoforms (ΔbioH1/2/3) renders M. smegmatis biotin auxotrophic. Along with the newly-identified Tam/BioC, the discovery of three unusual BioH isoforms defines an atypical 'BioC-BioH(3)' paradigm for the first-stage of mycobacterial biotin synthesis. This study solves a long-standing puzzle in mycobacterial nutritional immunity, providing an alternative anti-TB drug target.

Organizational Affiliation

Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People's Republic of China.

Macromolecule Content

Total Structure Weight: 182.71 kDa
Atom Count: 12,665
Modeled Residue Count: 1,654
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B, C, D, E A, B, C, D, E, F	282	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: NCTC7017_02293
UniProt
Find proteins for A0R6Y0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R6Y0 Go to UniProtKB: A0R6Y0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R6Y0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain I [auth B] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B]	I [auth B], L [auth D], N [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain M [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] J [auth C] K [auth D] M [auth E] G [auth A], H [auth B], J [auth C], K [auth D], M [auth E], O [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Focus chain O [auth F]