HAMAP rule MF_01258

General rule information [?]

Accession	MF_01258
Dates	21-APR-2005 (Created) 1-JUN-2023 (Last updated, Version 21)
Name	F420_ligase_CofE
Scope(s)	Archaea Archaeoglobi Halobacteria Methanobacteria Methanococci Methanomicrobia Methanopyri
Template(s)	Q58178 (COFE_METJA); O28028 (COFE_ARCFU); [ Recover all ]
Triggered by	HAMAP; MF_01258 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier	COFE
Protein name	RecName: Full=Coenzyme F420:L-glutamate ligase; EC=6.3.2.31; EC=6.3.2.34; AltName: Full=Coenzyme F420-0:L-glutamate ligase; AltName: Full=Coenzyme F420-1:gamma-L-glutamate ligase;
Gene name	Name=cofE;

Comments [?]

FUNCTION	Catalyzes the GTP-dependent successive addition of two or more gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8- didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form coenzyme F420- 0-glutamyl-glutamate (F420-2) or polyglutamated F420 derivatives.
CATALYTIC ACTIVITY	Reaction=GTP + L-glutamate + oxidized coenzyme F420-0 = GDP + H(+) + oxidized coenzyme F420-1 + phosphate; Xref=Rhea:RHEA:30555, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58189, ChEBI:CHEBI:59907, ChEBI:CHEBI:59920; EC=6.3.2.31;
CATALYTIC ACTIVITY	Reaction=GTP + L-glutamate + oxidized coenzyme F420-1 = GDP + H(+) + oxidized coenzyme F420-2 + phosphate; Xref=Rhea:RHEA:30523, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:57922, ChEBI:CHEBI:58189, ChEBI:CHEBI:59920; EC=6.3.2.34;
COFACTOR	Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 divalent metal cations per subunit. The ions could be magnesium and/or manganese.;
COFACTOR	Name=K(+); Xref=ChEBI:CHEBI:29103; Note=Monovalent cation. The ion could be potassium.;
PATHWAY	Cofactor biosynthesis; coenzyme F420 biosynthesis.
SUBUNIT	Homodimer.
SIMILARITY	Belongs to the CofE family.

Keywords [?]

Gene Ontology [?]

GO:0052618; Molecular function:coenzyme F420-0:L-glutamate ligase activity

GO:0052619; Molecular function:coenzyme F420-1:gamma-L-glutamate ligase activity

GO:0052645; Biological process:F420-0 metabolic process

Cross-references [?]

Pfam	PF01996; F420_ligase; 1;
NCBIfam	TIGR01916; F420_cofE; 1;

Features [?]

From: COFE_ARCFU (O28028)

Key

From

Description

Tag

Condition

FTGroup

BINDING

/ligand="GTP"
/ligand_id="ChEBI:CHEBI:37565"

[LIMV]-P-x-[IVEF]

BINDING

/ligand="GTP"
/ligand_id="ChEBI:CHEBI:37565"

[SEH]-T

BINDING

206

213

/ligand="GTP"
/ligand_id="ChEBI:CHEBI:37565"

BINDING

109

/ligand="a divalent metal cation"
/ligand_id="ChEBI:CHEBI:60240"
/ligand_label="1"

BINDING

150

/ligand="a divalent metal cation"
/ligand_id="ChEBI:CHEBI:60240"
/ligand_label="1"

BINDING

151

/ligand="a divalent metal cation"
/ligand_id="ChEBI:CHEBI:60240"
/ligand_label="2"

[TS]

BINDING

208

/ligand="a divalent metal cation"
/ligand_id="ChEBI:CHEBI:60240"
/ligand_label="2"

[EQ]

BINDING

/ligand="GTP"
/ligand_id="ChEBI:CHEBI:37565"

BINDING

112

/ligand="GTP"
/ligand_id="ChEBI:CHEBI:37565"

Additional information [?]

Size range	248-257 amino acids
Related rules	MF_01259
Fusion	Nter: None Cter: None
Comments	CofE homologs are found in the genomes of all organisms currently known to produce coenzyme F420. These include not only the methanogenic archaea but also nonmethanogenic archaea such as Halobacteria and Archaeoglobus, as well as some eubacteria such as Streptomyces, Mycobacterium, Nocardia, and Thermobifida (see MF_01259). The length of the polyglutamate tail varies in different organisms. According to PubMed:12867481 (Graupner et al., 2003) and PubMed:11479701 (Bair et al., 2001): Analyses of the F420s present in Methanococcus jannaschii have shown that these cells contain a series of gamma-glutamyl-linked F420s capped with a single, terminal alpha-linked L-glutamate. The predominant form of F420 was designated as alpha-F420-3 and represented 86% of the F420s in these cells. Analyses of Methanosarcina thermophila, Methanosarcina barkeri, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Mycobacterium smegmatis showed that they contained only gamma-glutamyl-linked F420s, with the following predominant forms: Methanosarcina thermophila (gamma-F420-3, 19%; gamma-F420-4, 62%), Methanosarcina barkeri (gamma-F420-2, 31%; gamma-F420-4, 32%), Methanobacterium thermoautotrophicum (gamma-F420-2, 80%), Archaeoglobus fulgidus (gamma-F420-4, 89%), and Mycobacterium smegmatis (gamma-F420-5, 67%; gamma-F420-6, 31%). In mycobacteria, the length of the polyglutamate tail varies by up to nine residues, with predominant species containing four to seven glutamate molecules (Bair et al., 2001, PubMed:11479701; Bashiri et al., 2008, PubMed:18434308).

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