Update of the NQO gene family UPDATE ON GENE COMPLETIONS ARNeDviAeNwNOTATIONS to the ﬂavodoxin-2 family (Pfam 02525) because they carry a domain having a ﬂavodoxin-like fold. The ﬂavodoxin-2 family is a member of the ﬂavoprotein clan. Based on the Pfam database deﬁnition: ‘A clan contains two or more Pfam families that have arisen from a single evolutionary origin. Evidence of their evolutionary relationship is usually determined by similar tertiary structures or, when structures are not available, by common sequence motifs.’25 The category of ‘clans’ is thus usually introduced in order to encompass two or more gene families that can be globally quite distant evolutionarily but have some segment of the gene products that show a high degree of similarity. Hence in a BLAST search, a sequence may signiﬁcantly hit more than one member of another family of the clan — as well as all members within one family. The ﬂavoprotein clan The ﬂavoprotein clan includes four Pfam members: ﬂavo- doxin-1, ﬂavodoxin-2, ﬂavodoxin NdrI and FMN red (Table 1). The ﬂavodoxin-1 family includes ﬂavodoxins and nitric oxide synthases. Members of this clan are composed of ﬂavin mononucleotide (FMN)- or ﬂavin adenine dinucleo- tide-binding redox proteins. Flavoproteins act in various electron transport systems as functional analogues of ferre- Table 1. Relationship of the NQO gene family to the ﬂavoprotein clan. Flavoprotein clan (four Pfam members) Flavodoxin-1 family Flavodoxins Nitric oxide synthases Flavodoxin-2 family Bacterial NQO3 genes Vertebrate NQO1, NQO2 genes Fungal NQO4 genes Archaebacterial NQO5 genes Flavodoxin Ndrl family Ribonucleotide reductases ﬂavin mononucleotide red family Flavin reductases Bacterial acyl carrier protein phosphodiesterase doxins; they are characterised by an open twisted alpha/beta structure consisting of ﬁve parallel beta-sheets connected by alpha-helices which surround the sheet. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group, and are function- ally interchangeable with ferredoxins. Flavodoxin genes are found in prokaryotes, cyanobacteria and some eukaryotic algae. Nitric oxide synthases (EC:1.14.13.39) produce nitric oxide from L-arginine and NADPH. Nitric oxide acts as a second messenger signalling molecule in the body. Five NOS genes have been found in the human genome: NOS1 (neuronal); NOS2A (hepatocyte inducible); NOS2B; NOS2C; and NOS3 (endothelial cell) (http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/). The ﬂavodoxin-2 family includes bacterial and eukaryotic NAD(P)H:quinone reductases (as described above), as well as the bacterial acyl carrier protein (ACP), phosphodiesterase (EC:3.1.4.14). The acyl carrier enzyme converts the holo-ACP into apo-ACP by catalysing the hydrolysis of the phosphodiester linkage between Ser-36 of ACP and the 40-phosphopantethein prosthetic group. ACP is a small (8.8 kDa) protein that plays a central role in the biosynthesis of fatty acids in bacteria, plant chloroplasts and other organisms. ACP phosphodiesterase is known to be encoded by the acpD gene in Escherichia coli and has been widely distributed in other bacteria, including Azospirillum brasilense, Bacillus halodurans, B. stearothermophilus, B. subtilis, Haemophilus inﬂuenzae, Lactococcus lactis, Mesorhizobium loti, Mycoplasma pneumoniae, Pseudomonas aeruginosa and Streptomyces coelicolor. The ﬂavodoxin_NdrI family contains ribonucleotide reductases, which are a family of complex enzymes that play an essential role in all organisms. These enzymes catalyse de novo synthesis of deoxyribonucleotides required for DNA replication and repair.26 Finally, members of the FMN red family (ﬂavin reductases) use ﬂavins as substrates and are distinct from ﬂavoenzymes, which have tightly bound ﬂavins. The reduced ﬂavin can serve to provide electrons for ferric ion complexes and iron proteins. In E. coli, reactivation of ribonucleotide reductase is achieved by the formation of reduced ﬂavins by ﬂavin reductase. Previous confusion about NQO genes and diaphorases Much of the confusion that has arisen with the nomenclature of NQO1, NQO2 and related proteins can be traced back to the widespread use of the term ‘diaphorase’ in enzymatic studies more than 50 years ago. In fact, this terminology is still being carried forward.27 The term ‘diaphorase’ has generally been used to describe a ‘coenzyme’ (often a ﬂavoprotein) that can transfer electrons from reduced pyridine nucleotides to electron acceptors.9,28 In any biological system, therefore, q HENRY STEWART PUBLICATIONS 1473-9542. HUMAN GENOMICS. VOL 2. NO 5. 329–335 MARCH 2006 331