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HAMAP rule MF_01258

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General rule information [?]

Accession MF_01258
Dates 21-APR-2005 (Created)
1-JUN-2023 (Last updated, Version 21)
Name F420_ligase_CofE
Scope
Archaea; Archaeoglobi
Archaea; Halobacteria
Archaea; Methanobacteria
Archaea; Methanococci
Archaea; Methanomicrobia
Archaea; Methanopyri
Templates Q58178 (COFE_METJA); O28028 (COFE_ARCFU): [Recover all]
Triggered by

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
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 RHEA:30555: GTP + L-glutamate + oxidized coenzyme F420-0 = GDP + H(+) + oxidized coenzyme F420-1 + phosphate
EC 6.3.2.31
RHEA:30523: GTP + L-glutamate + oxidized coenzyme F420-1 = GDP + H(+) + oxidized coenzyme F420-2 + phosphate
EC 6.3.2.34
Cofactor Mg(2+)
Mn(2+)
Note: Binds 2 divalent metal cations per subunit. The ions could be magnesium and/or manganese.
K(+)
Note: Monovalent cation. The ion could be potassium.
Pathway Cofactor biosynthesis; coenzyme F420 biosynthesis.
Subunit Homodimer.
Similarity Belongs to the CofE family.

Keywords [?]

GTP-binding
Ligase
Magnesium
Manganese
Metal-binding
Nucleotide-binding
Potassium

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     To       Description   Tag   Condition   FTGroup
BINDING     11     14       /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565     [LIMV]-P-x-[IVEF]  
BINDING     40     41       /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565     [SEH]-T  
BINDING     206     213       /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565        
BINDING     109     109       /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240" /ligand_label="1     D  
BINDING     150     150       /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240" /ligand_label="1     D  
BINDING     151     151       /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240" /ligand_label="2     [TS]  
BINDING     208     208       /ligand="a divalent metal cation" /ligand_id="ChEBI:CHEBI:60240" /ligand_label="2     [EQ]  
BINDING     45     45       /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565     K  
BINDING     112     112       /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565     N  

Additional information [?]

Size range 248-257 amino acids
Related rules MF_01259 (FBIB supersedes the current rule)
Fusion 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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