Table 2.

Predicted NAD-Binding Proteins by PatchSurfer2.0^a

proteinb	gene ID	PDB ID	co-crystallized ligand	ligand similarity to NAD (SIMCOMP score)c	GO term annotatedd	overlap with experimental resultsee
			predicted NAD-binding proteins
glyceraldehyde 3-phosphate dehydrogenase	gapA	1GAD	NAD	1.000	×	×
dTDB–glucose 4,6-dehydrogenase	rffG	1BXK	NAD	1.000
formate dehydrogenase H	fdhF	2IV2	molybdopterin guanine dinucleotide	0.517
β-ketoacyl–ACP reductase*	fabG	1Q7B	NADP	0.878	×
2,4-dienoyl–CoA reductase*	fadH	1PS9	NADP	0.878
quinone oxidoreductase*	qorA	1QOR	NADP	0.878
glutathione transferase	yghU	3C8E	glutathione	0.085		×
glycerol–3-phosphate dehydrogenase*	glpD	2QCU	FAD	0.470
methionine synthase	metH	1BMT	co-methylcobalamin	0.193
7-α-hydroxysteroid dehydrogenase*	hdhA	1FMC	NAD	1.000
nucleotidyltrasferase	galT	1GUQ	uridine-5′-diphosphate-glucose	0.483		×
purine nucleoside phosphorylase	deoD	1K9S	N7-methyl-formycin A	0.306		×
3-isopropylmalate dehydrogenase	leuB	1CM7			×	×
GTP cyclohydrolase	folE	1A8R	GTP	0.462
malonyl–CoA/ACP transcyclase	fabD	1MLA				×
2-methylcitrate dehydratase	prpD	1SZQ
glutathione reductase	gor	1GES	NAD	1.000
alkyl hydroperoxide reductase	ahpF	4O5Q	FAD	0.470	×
UDP–N-acetylmyramyl tripeptide synthase*	murE	1E8C	uridine-5′-diphosphate-N-acetylmuramoyl-l-alanine-d-glutamate	0.384
dihydrolipoamide hydrogenase	lpd	4JDR	FAD	0.470	×	×
			predicted NADP-binding proteins
GDP 4-keto-6-de-oxy-d-mannose epimerase reductase	fcl	1E6U	NADP	0.878
dihydrofolate reductase	folA	1RA9	NADP	0.878
2,4-dienoyl–CoA reductase*	fadH	1PS9	NADP	0.878
β-ketoacyl–ACP reductase*	fabG	1Q7B	NADP	0.878
GAR transformylase	purN	1JKX	N-[5′-O-phosphono-ribofuranosyl]-2-[2-hydroxy-2-[4-[glutamic acid]-N-carbonylphenyl]-3-[2-amino-4-hydroxy-quinazolin-6-Yl]-propanylamino]-acetamide	0.256
microcin C7 self-immunity protein	mccF	4IIY	5′-O-(α-glutamylsulfamoyl) inosine	0.333
UDP–N-acetylmyramyl tripeptide synthase*	murE	1E8C	uridine-5′-diphosphate-N-acetylmuramoyl-l-alanine-d-glutamate	0.384
glutamate racemase	murI	2JFN	uridine-5′-diphosphate-N-acetylmuramoyl-l-alanine	0.409
UDP–N-acetylmuramoyl l-alanine ligase	murC	2F00
glycerol-3-phosphate dehydrogenase*	glpD	2QCU	FAD	0.470
7-α-hydroxysteroid dehydrogenase*	hdhA	1FMC	NAD	1.000
UDP–l-Ara4N formyltransferase	arnA	1Z75			×
auccinyl–ALA–PRO–ALA–P-nitroanilide	ppiA	1V9T	succinyl–ALA–PRO–ALA–P-nitroanilide	0.098		×
threonyl–tRNA synthetase	thrS	1EVL	5′-O-(N-(l-threonyl)-sulfamoyl)adenosine	0.396
enoyl–ACP reductase	fabI	4JQC	NAD	1.000		×
MTA/SAH nucleosidase	mtnN	3O4V	(3R,4S)-4-(4-chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine	0.320		×
			predicted NADP-binding proteins
2,3-diketo-l-gulonate reductase	slr	1S2O			×
quinone oxidoreductase*	qorA	1QOR	NADP	0.878
ketopantoate hydroxymethyltransferase	panB	1M3U	ketopantoate	0.058		×
putative N-acetylmannosamin kinase	nanK	2AA4
pyridine nucleotide transhydrogenase	pntA	1X15	NAD	1.000	×
UDP–sugar hydrolase	ushA	1HP1	ATP	0.531		×

^aA protein was predicted as NAD-binding if either NAD or NADP was predicted within the top 10 scoring ligands for the protein.

^bThe proteins marked with asterisks are predicted both as NAD-binding (top half of the table) and NADP-binding (bottom half). There are six such proteins

^cSIMCOMP is software that compares and quantifies similarity between two chemical compounds by considering two-dimensional chemical structures of the compounds. The score ranges from 0.0 to 1.0, with 1.0 indicating the identical compounds.

^dThe GO term for NAD binding (GO: 0051288) in annotation in the UniProt database was examined.

^eA protein was checked if it was included in the list of the 78 detected NAD-binding proteins by pulse proteolysis.