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Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its product, 3-phospho-D-glycerate.

Lundqvist T, Schneider G
J Biol Chem 264 3643-6 (1989)
Cited: 12 times
EuropePMC logo PMID: 2492987

Abstract

The crystal structure of the binary complex of non-activated ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and its product 3-phospho-D-glycerate has been determined to 2.9-A resolution. This structure determination confirms the proposed location of the active site (Schneider, G., Lindqvist, Y., Brändén, C.-I., and Lorimer, G. (1986) EMBO J. 5, 3409-3415) at the carboxyl end of the beta-strands of the alpha/beta-barrel in the carboxyl-terminal domain. One molecule of 3-phosphoglycerate is bound per active site. All oxygen atoms of 3-phosphoglycerate form hydrogen bonds to groups of the enzyme. The phosphate group interacts with the sidechains of residues Arg-288, His-321, and Ser-368, which are conserved between enzymes from different species as well as with the main chain nitrogens from residues Thr-322 and Gly-323. These amino acid residues constitute one of the two phosphate binding sites of the active site. The carboxyl group interacts with the side chains of His-287, Lys-191, and Asn-111. Implications of the activation process for the binding of 3-phosphoglycerate are discussed.

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  2. Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces. Zhang S, Golbraikh A, Tropsha A. J Med Chem 49 2713-2724 (2006)
  3. Evolutionary plasticity of protein families: coupling between sequence and structure variation. Panchenko AR, Wolf YI, Panchenko LA, Madej T. Proteins 61 535-544 (2005)


Reviews citing this publication (1)

  1. Structure and function of Rubisco. Andersson I, Backlund A. Plant Physiol Biochem 46 275-291 (2008)

Articles citing this publication (8)

  1. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K. Structure 9 473-481 (2001)
  2. Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. Schneider G, Lindqvist Y, Lundqvist T. J Mol Biol 211 989-1008 (1990)
  3. Comparison of the crystal structures of L2 and L8S8 Rubisco suggests a functional role for the small subunit. Schneider G, Knight S, Andersson I, Brändén CI, Lindqvist Y, Lundqvist T. EMBO J 9 2045-2050 (1990)
  4. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Li H, Sawaya MR, Tabita FR, Eisenberg D. Structure 13 779-789 (2005)
  5. Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate. Newman J, Gutteridge S. Structure 2 495-502 (1994)
  6. Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense. Wu J, Meng X, Jiang W, Wang Z, Zhang J, Meng F, Yao X, Ye M, Yao L, Wang L, Yu N, Peng D, Xing S. Front Plant Sci 13 822374 (2022)
  7. Electrostatic fields at the active site of ribulose-1,5-bisphosphate carboxylase. Lu GG, Lindqvist Y, Schneider G. Proteins 12 117-127 (1992)
  8. Amino-terminal truncations of the ribulose-bisphosphate carboxylase small subunit influence catalysis and subunit interactions. Paul K, Morell MK, Andrews TJ. Plant Physiol 102 1129-1137 (1993)


Related citations provided by authors (5)

  1. Crystal Structure of the Ternary Complex of Ribulose-1,5-Bisphosphate Carboxylase, Mg(II), and Activator Co2 at 2.3-Angstroms Resolution. Lundqvist T, Schneider G Biochemistry 30 904- (1991)
  2. Crystallographic Refinement and Structure of Ribulose-1,5-Bisphosphate Carboxylase from Rhodospirillum Rubrum at 1.7 Angstroms Resolution. Schneider G, Lindqvist Y, Lundqvist T J. Mol. Biol. 211 989- (1990)
  3. Crystal Structure of the Complex of Ribulose-1,5-Bisphosphate Carboxylase and a Transition State Analogue, 2-Carboxy-D-Arabinitol 1,5-Bisphosphate. Lundqvist T, Schneider G J. Biol. Chem. 264 7078- (1989)
  4. Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase. Andersson I, Knight S, Schneider G, Lindqvist Y, Lundqvist T, Branden C-I, Lorimer GH Nature 337 229- (1989)
  5. Three-Dimensional Structure of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Rhodospirillum Rubrum at 2.9 Angstroms Resolution. Schneider G, Lindqvist Y, Branden C-I, Lorimer G EMBO J. 5 3409- (1986)

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