Database accession: MF7000995
Name: F420-gamma glutamyl ligase (Archaeoglobus fulgidus)
PDB ID: 2phn
Experimental method: X-ray (1.35 Å)
Assembly: Homodimer
Source organism: Archaeoglobus fulgidus
Primary publication of the structure:
Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A
Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.
(2007) J. Mol. Biol. 372: 456-69
PMID: 17669425
Abstract:
F(420) is a flavin-like redox-active coenzyme commonly used by archaea and some eubacteria in a variety of biochemical reactions in methanogenesis, the formation of secondary metabolites, the degradation of nitroaromatic compounds, activation of nitroimidazofurans, and F(420)-dependent photolysis in DNA repair. Coenzyme F(420)-2 biosynthesis from 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) and lactaldehyde involves six enzymatic steps and five proteins (CofA, CofB, CofC, CofD, and CofE). CofE, a F(420)-0:gamma-glutamyl ligase, is responsible for the last two enzymatic steps; it catalyses the GTP-dependent addition of two L-glutamate residues to F(420)-0 to form F(420)-2. CofE is found in archaea, the aerobic actinomycetes, and cyanobacteria. Here, we report the first crystal structure of the apo-F(420)-0:gamma-glutamyl ligase (CofE-AF) from Archaeoglobus fulgidus and its complex with GDP at 2.5 A and 1.35 A resolution, respectively. The structure of CofE-AF reveals a novel protein fold with an intertwined, butterfly-like dimer formed by two-domain monomers. GDP and Mn(2+) are bound within the putative active site in a large groove at the dimer interface. We show that the enzyme adds a glutamate residue to both F(420)-0 and F(420)-1 in two distinct steps. CofE represents the first member of a new structural family of non-ribosomal peptide synthases.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
coenzyme F420-0 coenzyme F420-0:L-glutamate ligase activity
coenzyme F420-1 coenzyme F420-1:gamma-L-glutamate ligase activity
GTP binding GTP binding
metal ion binding metal ion binding
Biological process:
F420-0 metabolic process F420-0 metabolic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Coenzyme F420:L-glutamate ligase
Source organism: Archaeoglobus fulgidus
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL
UniProtKB AC: O28028 (positions: 2-249)
Coverage: 99%
Name: Coenzyme F420:L-glutamate ligase
Source organism: Archaeoglobus fulgidus
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL
UniProtKB AC: O28028 (positions: 1-249)
Coverage: 100%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The F420-gamma glutamyl ligase forms a tightly packed, highly intertwined, butterfly-like dimer formed by two-domain monomers. The dimer interface is very extensive and the putative active site lies in a large groove at the dimer interface. Also, the protein is a dimer in solution (SEC) which is in good agreement with its tight packing (PMID:17669425).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the MFIB database.
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