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231  structures 8277  species 0  interactions 76702  sequences 1007  architectures

Clan: FAD_Lum_binding (CL0076)

Summary

Riboflavin synthase/Ferredoxin reductase FAD binding domain Add an annotation

Riboflavin nucleotide coenzymes and flavin adenine dinucleotide (FAD) are essential cofactors for a large number of flavoproteins involved in a diverse set of redox reactions. There are thought to be four different FAD-binding folds [1].The FAD-binding fold of this clan is a cylindrical beta-fold. More specifically, the domain forms a flattened six-stranded antiparallel beta-barrel organised into two orthogonal sheets (1-2-5 and 4-3-6) separated by one alpha-helix. The cylinder is open between strands strand 4 and 5. This opening of the cylinder makes space for the isoalloxazine and ribityl moieties of the FAD, to which hydrogen bonds are formed from the open edges of the strands. The other end of the cylinder is covered by the only helix of the domain, which is essential for the binding of the pyrophosphate groups of the FAD [1].The structural differences in the FAD-binding domain are manifested mainly as loops of different length and extra extending structural elements, which may be important for interactions with their redox partners [1]. The structural core of all clan members is highly conserved.

This clan contains 5 families and the total number of domains in the clan is 76702. The clan was built by RD Finn.

Literature references

  1. Dym O, Eisenberg D; , Protein Sci 2001;10:1712-1728.: Sequence-structure analysis of FAD-containing proteins. PUBMED:11514662 EPMC:11514662

Members

This clan contains the following 5 member families:

FAD_binding_1 FAD_binding_6 FAD_binding_8 FAD_binding_9 Lum_binding

External database links

CATH: 2.40.30.10 1.20.990.10
SCOP: 63380

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
FAD_binding_6 (PF00970) 27590 (36.0%) View
Lum_binding (PF00677) 16593 (21.6%) View
FAD_binding_8 (PF08022) 14903 (19.4%) View
FAD_binding_1 (PF00667) 12101 (15.8%) View
FAD_binding_9 (PF08021) 5515 (7.2%) View
Total: 5 Total: 76702 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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