Table 1.

Biochemical identity and composition of large macromolecular complexes purified from Desulfovibrio vulgaris Hildenborough by the tagless strategy

Gene*	Database annotation	EC number	Molecular mass of polypeptide, kDa	Particle weight estimated by SEC (weight estimated from EM structure when known) (kDa)	Approx. no. of particles per cell	Stoichiometry (symmetry when known)†	Examples of stoichiometry in other bacteria‡
DVU0460	Predicted phospho-2-dehydro-3-deoxyheptonate aldolase	2.5.1.54 or 4.1.2.13	28.4	530	200	α16–20	α10§
DVU0631	Putative protein	—	55.7	600	100	α10–14	—
DVU0671	Putative protein	—	59.1	440 (473)	700	α8, (D4)	—
DVU1012	Hemolysin-type calcium-binding repeat protein	—	316.4	800	1,400	α2–3	—
DVU1044	Inosine-5′-monophosphate dehydrogenase	1.1.1.205	52.2	440 (418)	800	α8 (D4)	α4
DVU1198	Lumazine synthase (riboflavin synthase β-subunit)	2.5.1.9	16.6	600 (996)¶	300	α?β60 (I)	α3β60 (15); β5 (29); β10 (30)
DVU1200	Riboflavin synthase α-subunit		23.6
DVU1329	RNA polymerase β-subunit	2.7.7.6	153.2	1,100 (885)	500	[ββ′α2ωNusA]2 (C2)	ββ′α2ω
DVU2928	RNA polymerase β′-subunit		154.8
DVU2929	RNA polymerase α-subunit		38.9
DVU3242	RNA polymerase ω-subunit		8.8
DVU0510	NusA		47.8
DVU1378	Ketol-acid reductoisomerase	1.1.1.86	36.1	370	600	α8–12	α4; α12 (31)
DVU1833	Phosphoenolpyruvate synthase	2.7.9.2	132.6	370 (265)	1,200	α2 (C2)	α2
DVU1834	Pyruvate carboxylase‖	6.4.1.1	136.4	340	800	[αβ]2 or [αβ]4**	[αβ]4 (32); [αβ]4 (33); [αβ]12 (34)
DVU1976	60 kDa chaperonin (GroEL)	—	58.4	530 (409 and 818)	700††	α7 and [α7]2 (C7 and D7)	[α7]2
DVU2349	Carbohydrate phosphorylase	2.4.1.1	97.4	670 (≥584)	700	α6–7 (Ring-shaped)	α2
DVU2405	Alcohol dehydrogenase	1.1.1.1	41.8	370	12,000	α9–10	α2
DVU3025	Pyruvate:ferredoxin oxidoreductase ‡‡	1.2.7.1	131.5	1,000 (1,052)	4,000	[αβδγ]8, (D4)	[αβδγ]2; [αβδγ]; (35)
DVU3319	Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase	1.5.99.8 and 1.5.1.12	119.0	300	1100	α3	α2; α2 or α4 (36)

Homologs from other bacteria listed in the rightmost column are members of the same Pfam families (28) as the D. vulgaris protein.

*Entries in bold font indicate protein complexes for which three-dimensional reconstructions were obtained by single-particle electron microscopy (EM) of negatively stained samples.

^†Stoichiometry is derived from EM data where we have determined the structure. In other cases, the stochiometry is derived from the SEC size estimation.

^‡Unless indicated by a specific literature citation, information about subunit stoichiometry was obtained from http://biocyc.org

^§E. coli also contains three DAHP synthetases (AroF, AroH and AroG) with stoichiometry α₂,α₂ and α₄, respectively. M. tuberculosis AroG has stoichiometry α₅(29). Although Pfam lists Class I aldolases such as DVU0460 in a different family than DAHP synthetases, they are all classified in the same superfamily (Aldolase) in SCOP (37), based on structural evidence of remote homology.

^¶Contribution of the Riboflavin synthase α-subunit to the particle weight is not included.

^‖ Pyruvate carboxylase is present in some bacteria as a single polypeptide chain and in other bacteria as α and β chains that are homologous to the C- and N- terminal parts, respectively, of the single-chain form of the enzyme. In cases shown here, the α and β chains from other bacteria comprise the same Pfam domains as the single DvH protein. We use αβ to represent the single-chain form.

**EM result indicates either a dimer or tetramer. Size-exclusion chromatography cannot distinguish between these possibilities.

^†† Particle copy number estimated on the assumption that the protein is present in the cell as a D7 14-mer rather than as the C7 heptamer isolated in our standard buffer conditions.

^‡‡Homologs of pyruvate: ferredoxin oxidoreductase are sometimes fused and sometimes split into multiple chains. In the case shown here, the α, β, γ, and δ chains from T. maritima comprise the same Pfam domains as the single DvH protein. We use αβδγ to represent the single-chain form.