The light-harvesting complex 1-reaction center (LH1-RC) photosystem of the thermophilic purple sulfur bacterium Thermochromatium (Tch.) tepidum exhibits a near-infrared LH1-Q_y absorption band at 915 nm as regulated by binding calcium ions (Ca²⁺). To further explore the possible involvement of the C-terminal lysine residues of the LH1 α-polypeptide, we have genetically engineered a Rhodospirillum rubrum mutant strain to yield the site-directed modifications of the terminal α-Lys60 and α-Lys61 residues of Tch. tepidum LH1 α-polypeptide. Four of the LH1 mutants exhibit a subtle blue shift of 3 nm upon deletion or substitution of the lysine residues, however, they display over 40 nm blue shifts upon Ca²⁺ removal by ethylene diamine tetraacetic acid (EDTA) treatment. Spectral properties of native Tch. tepidum LH1-RC, the LH1-only, and the mutant LH1-only complexes are compared on a structural basis, which allows us to conclude that the C-terminal lysine residues and the Ca²⁺ binding synergistically affect the structural integrity and the LH1-Q_y spectral shift. This work demonstrates a methodology for the genetic manipulation of photosynthetic proteins lacking mutagenesis information, and may shed light on understanding the detailed structural factors involved in tuning the LH1-Q_y absorption.