High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii-An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle

被引:7
作者
Le Moigne, Theo [1 ,2 ]
Crozet, Pierre [1 ,3 ]
Lemaire, Stephane D. [1 ,4 ]
Henri, Julien [1 ]
机构
[1] Sorbonne Univ, CNRS, Lab Biol Mol & Cellulaire Eucaryotes, UMR8226,Inst Biol Physicochim, F-75005 Paris, France
[2] Univ Paris Saclay, Doctoral Sch Plant Sci, Fac Sci, F-91190 St Aubin, France
[3] Sorbonne Univ, Polytech Sorbonne, 4 Pl Jussieu, F-75005 Paris, France
[4] Sorbonne Univ, Inst Biol Paris Seine, CNRS, Lab Biol Computat & Quantitat,UMR7238, 4 Pl Jussieu, F-75005 Paris, France
关键词
photosynthesis; chloroplast; Calvin– Benson cycle; protein structure; X-ray crystallography; ribose isomerase; post-translational modification; redox; oligomerization; protein complexes; PENTOSE-PHOSPHATE PATHWAY; D-RIBOSE-5-PHOSPHATE ISOMERASE; REFINEMENT; METABOLISM; ACTIVATION; PREDICTION; SOFTWARE; REVEALS;
D O I
10.3390/ijms21207787
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Calvin-Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse post-translational modifications including phosphorylation and thiol-based modifications to presumably adjust its activity to the photosynthetic electron flow. Here, we describe the first experimental structure of a photosynthetic RPI at 1.4 angstrom resolution. Our structure confirms the composition of the catalytic pocket of the enzyme. We describe the homo-dimeric state of the protein that we observed in the crystal and in solution. We also map the positions of previously reported post-translational modifications and propose mechanisms by which they may impact the catalytic parameters. The structural data will inform the biochemical modeling of photosynthesis.
引用
收藏
页码:1 / 15
页数:15
相关论文
共 55 条
  • [1] PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution
    Adams, Paul D.
    Afonine, Pavel V.
    Bunkoczi, Gabor
    Chen, Vincent B.
    Davis, Ian W.
    Echols, Nathaniel
    Headd, Jeffrey J.
    Hung, Li-Wei
    Kapral, Gary J.
    Grosse-Kunstleve, Ralf W.
    McCoy, Airlie J.
    Moriarty, Nigel W.
    Oeffner, Robert
    Read, Randy J.
    Richardson, David C.
    Richardson, Jane S.
    Terwilliger, Thomas C.
    Zwart, Peter H.
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 : 213 - 221
  • [2] The Phenix software for automated determination of macromolecular structures
    Adams, Paul D.
    Afonine, Pavel V.
    Bunkoczi, Gabor
    Chen, Vincent B.
    Echols, Nathaniel
    Headd, Jeffrey J.
    Hung, Li-Wei
    Jain, Swati
    Kapral, Gary J.
    Kunstleve, Ralf W. Grosse
    McCoy, Airlie J.
    Moriarty, Nigel W.
    Oeffner, Robert D.
    Read, Randy J.
    Richardson, David C.
    Richardson, Jane S.
    Terwilliger, Thomas C.
    Zwart, Peter H.
    [J]. METHODS, 2011, 55 (01) : 94 - 106
  • [3] Towards automated crystallographic structure refinement with phenix.refine
    Afonine, Pavel V.
    Grosse-Kunstleve, Ralf W.
    Echols, Nathaniel
    Headd, Jeffrey J.
    Moriarty, Nigel W.
    Mustyakimov, Marat
    Terwilliger, Thomas C.
    Urzhumtsev, Alexandre
    Zwart, Peter H.
    Adams, Paul D.
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 : 352 - 367
  • [4] Establishment of publicly available cDNA material and information resource of Chlamydomonas reinhardtii (Chlorophyta) to facilitate gene function analysis
    Asamizu, E
    Nakamura, Y
    Miura, K
    Fukuzawa, H
    Fujiwara, S
    Hirono, M
    Iwamoto, K
    Matsuda, Y
    Minagawa, J
    Shimogawara, K
    Takahashi, Y
    Tabata, S
    [J]. PHYCOLOGIA, 2004, 43 (06) : 722 - 726
  • [5] BENSON AA, 1952, J BIOL CHEM, V196, P703
  • [6] Ribose-5-phosphate isomerases: characteristics, structural features, and applications
    Chen, Jiajun
    Wu, Hao
    Zhang, Wenli
    Mu, Wanmeng
    [J]. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 104 (15) : 6429 - 6441
  • [7] MolProbity: all-atom structure validation for macromolecular crystallography
    Chen, Vincent B.
    Arendall, W. Bryan, III
    Headd, Jeffrey J.
    Keedy, Daniel A.
    Immormino, Robert M.
    Kapral, Gary J.
    Murray, Laura W.
    Richardson, Jane S.
    Richardson, David C.
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 : 12 - 21
  • [8] Status of the crystallography beamlines at synchrotron SOLEIL
    Coati, A.
    Chavas, L. M. G.
    Fontaine, P.
    Foos, N.
    Guimaraes, B.
    Gourhant, P.
    Legrand, P.
    Itie, J. -P.
    Fertey, P.
    Shepard, W.
    Isabet, T.
    Sirigu, S.
    Solari, P. -L.
    Thiaudiere, D.
    Thompsona, A.
    [J]. EUROPEAN PHYSICAL JOURNAL PLUS, 2017, 132 (04):
  • [10] PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Dolinsky, Todd J.
    Czodrowski, Paul
    Li, Hui
    Nielsen, Jens E.
    Jensen, Jan H.
    Klebe, Gerhard
    Baker, Nathan A.
    [J]. NUCLEIC ACIDS RESEARCH, 2007, 35 : W522 - W525