A photosystem I (PS I) complex containing plastoquinone-9 (PQ-9) but devoid of F X , F B , and F A was isolated and characterized from a mutant strain of Synechococcus sp. PCC 7002 in which the menB and rubA genes were insertionally inactivated. In isolated PS I trimers, the decay of P700؉ measured in the near-IR and the decay of A 1 ؊ measured in the near-UV were found to be biphasic, with (averaged) room temperature lifetimes of 12 and 350 s. The decay-associated spectra of both kinetic phases are characteristic of the oxidized minus reduced difference spectrum of a semiquinone, consistent with charge recombination between P700؉ and PQ-9 ؊ . The amplitude of the flash-induced absorbance changes in both the near-IR and the near-UV show that approximately one-half of the A 1 binding sites are either empty or nonfunctional. A spin-polarized chlorophyll triplet is observed by time-resolved EPR, and it is attributed to the 3 P700 product of P700 ؉ A 0 ؊ charge recombination via the T 0 spin level in those PS I complexes that do not contain a functional quinone. In those A 1 sites that are occupied, the P700 ؉ Q ؊ polarization pattern indicates that PQ-9 is oriented in a similar manner to that in the menB mutant. When excess 9,10-anthraquinone is added in vitro, it displaces PQ-9 and occupies the A 1 binding site more readily than in the menB mutant. This can be explained by a greater accessibility to the A 1 site in the menB rubA mutant due to the absence of F X and the stromal ridge polypeptides. The relatively low binding affinity of 9,10-anthraquinone allows it to be readily removed from the A 1 site by washing. However, all A 1 sites are shown to bind napthoquinones with high affinity and thus are proven to be functionally competent in quinone binding. The ability to readily displace PQ-9 from the A 1 site makes the menB rubA mutant ideal for introducing novel quinones, particularly anthraquinones, into PS I.Photosystem I is a multisubunit, pigment-protein complex that is found in the membranes of plants, algae, and cyanobacteria and that mediates the light-induced transfer of electrons from plastocyanin/cytochrome c 6 to ferredoxin/flavodoxin. According to current understanding, light-induced charge separation results in the oxidation of the primary electron donor P700 (E m Ј ϩ430 mV), a chlorophyll a/aЈ heterodimer located on the luminal (inner) side of the membrane, and the reduction of the primary electron acceptor A 0 (E m Ј approximately Ϫ1000 mV), a chlorophyll a monomer located in the interior of the membrane. The electron is passed to A 1 (E m Ј approximately Ϫ800 mV), an alkyl-substituted menadione (2-methyl-1,4-naphthalenedione); to F X (E m Ј Ϫ705 mV), an interpolypeptide (4Fe-4S) cluster; and finally to F A (E m Ј Ϫ520 mV) and F B (E m Ј Ϫ580 mV), which are (4Fe-4S) clusters bound to the extrinsic subunit PsaC located on the stromal (cytoplasmic) side of the membrane. In most organisms, including Synechocystis sp. PCC 6803, the quinone in the A 1 site is phylloquinone (2-methyl-3-phytyl-1,4-naphtho...