PDBsum entry 4xom

Unknown function

PDB id: 4xom

Contents

Protein chains

206 a.a.

193 a.a.

178 a.a.

Ligands

SO4 ×2

Waters ×240

PDB id:

4xom

Name:

Unknown function

Title:

Coenzyme f420:l-glutamate ligase (fbib) from mycobacterium tuberculosis (c-terminal domain).

Structure:

Coenzyme f420:l-glutamate ligase. Chain: a, b, c, d. Fragment: unp residues 245-448. Engineered: yes

Source:

Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: h37rv. Cell_line: 25618. Gene: fbib, rv3262. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.233 R-free: 0.268

Authors:

A.M.Rehan,G.Bashiri,H.M.Baker,E.N.Baker,C.J.Squire

Key ref:

G.Bashiri et al. (2016). Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis. J Biol Chem, 291, 6882-6894. PubMed id: 26861878 DOI: 10.1074/jbc.M115.689026

Date:

16-Jan-15 Release date: 17-Feb-16

Protein chains

P9WP79  (FBIB_MYCTU) -  Bifunctional F420 biosynthesis protein FbiB from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 448 a.a.

Struc: 206 a.a.*

Protein chain

P9WP79  (FBIB_MYCTU) -  Bifunctional F420 biosynthesis protein FbiB from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 448 a.a.

Struc: 193 a.a.

Protein chain

P9WP79  (FBIB_MYCTU) -  Bifunctional F420 biosynthesis protein FbiB from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 448 a.a.

Struc: 178 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.1.3.8.17 - dehydro coenzyme F420 reductase.
• Reaction: oxidized coenzyme F420-0 + FMN + H⁺ = dehydro coenzyme F420-0 + FMNH2
• Enzyme class 2: Chains A, B, C, D: E.C.6.3.2.31 - coenzyme F420-0:L-glutamate ligase.
• Reaction: oxidized coenzyme F420-0 + GTP + L-glutamate = oxidized coenzyme F420-1 + GDP + phosphate + H⁺
• Enzyme class 3: Chains A, B, C, D: E.C.6.3.2.34 - coenzyme F420-1:gamma-L-glutamate ligase.
• Reaction: oxidized coenzyme F420-1 + GTP + L-glutamate = oxidized coenzyme F420-2 + GDP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M115.689026

J Biol Chem 291:6882-6894 (2016)

PubMed id: 26861878

Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis.

G.Bashiri, A.M.Rehan, S.Sreebhavan, H.M.Baker, E.N.Baker, C.J.Squire.

ABSTRACT

Cofactor F420is an electron carrier with a major role in the oxidoreductive reactions ofMycobacterium tuberculosis, the causative agent of tuberculosis. A γ-glutamyl ligase catalyzes the final steps of the F420biosynthesis pathway by successive additions ofl-glutamate residues to F420-0, producing a poly-γ-glutamate tail. The enzyme responsible for this reaction in archaea (CofE) comprises a single domain and produces F420-2 as the major species. The homologousM. tuberculosisenzyme, FbiB, is a two-domain protein and produces F420with predominantly 5-7l-glutamate residues in the poly-γ-glutamate tail. The N-terminal domain of FbiB is homologous to CofE with an annotated γ-glutamyl ligase activity, whereas the C-terminal domain has sequence similarity to an FMN-dependent family of nitroreductase enzymes. Here we demonstrate that full-length FbiB adds multiplel-glutamate residues to F420-0in vitroto produce F420-5 after 24 h; communication between the two domains is critical for full γ-glutamyl ligase activity. We also present crystal structures of the C-terminal domain of FbiB in apo-, F420-0-, and FMN-bound states, displaying distinct sites for F420-0 and FMN ligands that partially overlap. Finally, we discuss the features of a full-length structural model produced by small angle x-ray scattering and its implications for the role of N- and C-terminal domains in catalysis.