Crystal structures of the photosystem II D1 C-terminal processing protease

We report here the first three-dimensional structure of the D1 C-terminal processing protease (D1P), which is encoded by the ctpA gene. This enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II of oxygenic photosynthesis. Proteolytic processing is necessary to allow the light driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. The X-ray structure of the Scenedesmus obliquus enzyme has been determined at 1.8 Å resolution using the multiwavelength anomalous dispersion method. The enzyme is monomeric and is composed of three folding domains. The middle domain is topologically homologous to known PDZ motifs and is proposed to be the site at which the substrate C-terminus binds. The remainder of the substrate likely extends across the face of the enzyme, interacting at its scissile bond with the enzyme active site Ser 372 / Lys 397 catalytic dyad, which lies at the center of the protein at the interface of the three domains.

[1]  R. Liddington,et al.  Crystal structure of a PDZ domain , 1996, Nature.

[2]  W A Hendrickson,et al.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three‐dimensional structure. , 1990, The EMBO journal.

[3]  Suzanne Fortier,et al.  Direct methods for solving macromolecular structures , 1998 .

[4]  M. Paetzel,et al.  Crystal structure of a bacterial signal peptidase in complex with a β-lactam inhibitor , 1998, Nature.

[5]  Y. Yamamoto,et al.  Cloning, mapping, and characterization of the Escherichia coli prc gene, which is involved in C-terminal processing of penicillin-binding protein 3 , 1991, Journal of bacteriology.

[6]  W Furey,et al.  PHASES-95: a program package for processing and analyzing diffraction data from macromolecules. , 1997, Methods in enzymology.

[7]  J. W. Little,et al.  Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[8]  B. Diner,et al.  Role of the carboxy terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: assembly requires a free carboxyl group at C-terminal position 344. , 1992, Biochemistry.

[9]  R. Sauer,et al.  Identification of Active Site Residues of the Tsp Protease * , 1995, The Journal of Biological Chemistry.

[10]  D. Tronrud Conjugate-direction minimization: an improved method for the refinement of macromolecules. , 1992, Acta crystallographica. Section A, Foundations of crystallography.

[11]  H. Pakrasi,et al.  Molecular cloning and characterization of the ctpA gene encoding a carboxyl-terminal processing protease. Analysis of a spontaneous photosystem II-deficient mutant strain of the cyanobacterium Synechocystis sp. PCC 6803. , 1994, The Journal of biological chemistry.

[12]  M. Murcko,et al.  Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4A Cofactor Peptide , 1996, Cell.

[13]  S. Bron,et al.  Proteolysis in Cell Functions , 1997 .

[14]  M. A. Taylor,et al.  Processing of the D1 polypeptide of the photosystem II reaction centre and photoactivation of a low fluorescence mutant (LF‐1) of Scenedesmus obliquus , 1988 .

[15]  E. G. Frank,et al.  Structure of the UmuD′ protein and its regulation in response to DNA damage , 1996, Nature.

[16]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.

[17]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[18]  B. Diner,et al.  The D1 C-terminal processing protease of photosystem II from Scenedesmus obliquus. Protein purification and gene characterization in wild type and processing mutants. , 1997, The Journal of biological chemistry.

[19]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[20]  R. Sauer,et al.  Tsp: a tail-specific protease that selectively degrades proteins with nonpolar C termini. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[22]  R. Dalbey,et al.  A serine and a lysine residue implicated in the catalytic mechanism of the Escherichia coli leader peptidase. , 1993, The Journal of biological chemistry.

[23]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[24]  C P Ponting,et al.  Evidence for PDZ domains in bacteria, yeast, and plants , 1997, Protein science : a publication of the Protein Society.

[25]  M. Paetzel,et al.  Catalytic hydroxyl/amine dyads within serine proteases. , 1997, Trends in biochemical sciences.

[26]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[27]  S. N. Slilaty,et al.  The role of electrostatic interactions in the mechanism of peptide bond hydrolysis by a Ser-Lys catalytic dyad. , 1991, Protein engineering.

[28]  M. Seibert,et al.  Failure to Process the D1 Protein Inhibits the Oxidizing Side of PSII but not the Reaction Center or Reducing Side Reactions: Analysis of the LF-1 Mutant of Scenedesmus , 1987 .

[29]  J. Peng,et al.  Substrate recognition through a PDZ domain in tail-specific protease. , 2000, Biochemistry.

[30]  K. Satoh,et al.  Chromatographic purification and determination of the carboxy-terminal sequences of photosystem II reaction center proteins, Dl and D2 , 1990 .

[31]  C. Betzel,et al.  Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution , 1992, Nature.

[32]  S. Golden,et al.  psbA genes indicate common ancestry of prochlorophytes and chloroplasts , 1989, Nature.

[33]  John H. Lewis,et al.  Crystal Structures of a Complexed and Peptide-Free Membrane Protein–Binding Domain: Molecular Basis of Peptide Recognition by PDZ , 1996, Cell.

[34]  M. Takahashi,et al.  COOH‐terminal residues of D1 and the 44 kDa CPa‐2 at spinach photosystem II core complex , 1988, FEBS letters.

[35]  B. Diner,et al.  Expression of a higher plant psbA gene in Synechocystis 6803 yields a functional hybrid photosystem II reaction center complex. , 1991, The Plant cell.