PDBsum entry 1fc7

Hydrolase

PDB id: 1fc7

Contents

Protein chain

386 a.a. *

Waters ×325

* Residue conservation analysis

PDB id:

1fc7

Name:

Hydrolase

Title:

Photosystem ii d1 c-terminal processing protease

Structure:

Photosystem ii d1 protease. Chain: a. Fragment: residues 77-464. Synonym: d1 c-terminal processing protease. Engineered: yes

Source:

Scenedesmus obliquus. Organism_taxid: 3088. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.187 R-free: 0.267

Authors:

D.I.Liao,J.Qian,D.A.Chisholm,D.B.Jordan,B.A.Diner

Key ref:

D.I.Liao et al. (2000). Crystal structures of the photosystem II D1 C-terminal processing protease. Nat Struct Biol, 7, 749-753. PubMed id: 10966643 DOI: 10.1038/78973

Date:

18-Jul-00 Release date: 18-Jan-01

Protein chain

O04073  (CTPA_TETOB) -  C-terminal processing peptidase, chloroplastic from Tetradesmus obliquus

Seq: 464 a.a.

Struc: 386 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.102 - C-terminal processing peptidase.
• Reaction: The enzyme shows specific recognition of a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr, and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. A typical cleavage is -Ala-Ala-|-Arg-Ala-Ala-Lys-Glu-Asn-Tyr-Ala-Leu-Ala-Ala. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II.

DOI no: 10.1038/78973

Nat Struct Biol 7:749-753 (2000)

PubMed id: 10966643

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

D.I.Liao, J.Qian, D.A.Chisholm, D.B.Jordan, B.A.Diner.

ABSTRACT

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 A 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.

Selected figure(s)

Figure 1.
Figure 1. Structure of D1 protease. a, Ribbon drawing of D1P. The A domain is in red, the B domain in yellow and the C domain in blue. The extended -hairpin loop from the C domain forms an integral part of the folding domain A and is regarded as part of that domain. The loops that connect domains A to B and B to C have very high temperature factors and are colored in green. The side chains of the residues involved in catalysis or substrate binding, K397, S372 and R247, are shown in ball-and-stick representation. The GVGL loop in the B domain, highlighted in magenta, has been shown to be involved in the binding of the C-terminal residues of the peptide ligand in the structurally homologous third PDZ domain of synaptic protein PSD-95^25. b, Stereo view of the C trace of D1P. Every 10^th residue and the N-terminus and C-terminus are labeled. The disulfide bond between Cys 260 and Cys 451 is shown in yellow. The orientation of the molecule is the same as the standard orientation in (a).

Figure 4.
Figure 4. The PDZ domain. a, Schematic diagram of the secondary structures of the B domain of D1P (upper) and the third PDZ domain of human D1gA (PDB accession code 1PDR, residues 463 -544)24, the third PDZ domain of the synaptic protein PSD-95 (1KWA, residues 487 -570)25 and the PDZ domain of neuronal nitric oxide synthase (1QAU, residues 14 -101)26. The location of the conserved Arg/Lys (Arg 247 in D1P, Arg 471 in 1PDR, Lys 495 in 1KWA and Arg 23 in 1QAU) is marked by a red circle. The location of the GLGF repeat of the carboxylate binding loop in 1PDR and 1QAU (GVGL in D1P and PMGL in 1KWA) is labeled by a yellow circle. Their three-dimensional structures are also very similar. The r.m.s.d. for C atoms between D1P and 1PDR is 1.5 Å using 76 matching residues for the alignment. The r.m.s.d. is 1.79 Å for 81 matching pairs of C atoms between D1P and 1QAU. For D1P and 1KWA, the r.m.s.d. is 1.9 Å for 71 matching pairs. b, The conserved Arg 247 in the B domain of D1P. The side chain of Arg 247 is partially buried with a solvent accessible area of 23 Å2.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 749-753) copyright 2000.

Figures were selected by the author.